From chemistry-request@server.ccl.net Thu Apr 11 16:09:47 2002 Received: from web13402.mail.yahoo.com ([216.136.175.60]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g3BK9kj22922 for ; Thu, 11 Apr 2002 16:09:47 -0400 Message-ID: <20020411200933.79038.qmail@web13402.mail.yahoo.com> Received: from [67.17.165.2] by web13402.mail.yahoo.com via HTTP; Thu, 11 Apr 2002 13:09:33 PDT Date: Thu, 11 Apr 2002 13:09:33 -0700 (PDT) From: quch quch Subject: standard dataset for docking. To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello, Is there any standard (or acceptable) docked datasets available for comparing different score functions? thanks, qc __________________________________________________ Do You Yahoo!? Yahoo! Tax Center - online filing with TurboTax http://taxes.yahoo.com/ From chemistry-request@server.ccl.net Thu Apr 11 18:54:43 2002 Received: from rm-rstar.sfu.ca (root@[142.58.120.21]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3BMsgj26772 for ; Thu, 11 Apr 2002 18:54:42 -0400 Received: from fraser.sfu.ca (johnsont@fraser.sfu.ca [142.58.101.25]) by rm-rstar.sfu.ca (8.10.1/8.10.1/SFU-5.0H) with ESMTP id g3BMsWS21313; Thu, 11 Apr 2002 15:54:36 -0700 (PDT) Received: from localhost (johnsont@localhost) by fraser.sfu.ca (8.9.2/8.9.2/SFU-5.0C) with ESMTP id PAA28127; Thu, 11 Apr 2002 15:54:31 -0700 (PDT) X-Authentication-Warning: fraser.sfu.ca: johnsont owned process doing -bs Date: Thu, 11 Apr 2002 15:54:31 -0700 (PDT) From: Margaret Johnson To: "X. Tan" cc: chemistry@ccl.net Subject: Re: CCL:torsion constraints in autodock In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Xiaojian, The hardtorcon command doesn't work for me either. It would be great if someone out there has some suggestions. I'm not quite sure of the structure you're talking about there. When you run deftors, usually the default is to have the -a flag on, which tells the program to automatically set amide bond torsions as inactive. If it's not an amide bond then you could try leaving it inactive. If there's a reason why you do want the torsion semi-flexible and not fixed, the only way I've been able to do this, so far, is to use "gausstorcon" with a high energy barrier, e.g. 100 or higher, and small half-width, e.g. 10-20 degrees. This usually gives a variation of about +/- 5 degrees in the torsion. I don't know how/when this barrier is applied in the calculation though. > > I wondered whether I gave the wrong constraint. For a > torsion A-B-C-D, in autodock program, the rotatable bond is defined by two > atoms(B-C), then where the A and D come from, and is it possible to assign > the torsion angle unambiguously in the constraints? How to do that? I think the program uses general conventions for defining torsions... for example, if there are two possible heavy atoms, it would use the one with higher priority to define the torsion, e.g. O rather than C. But I'm not sure about that. However, you can check this using your output structures, as the torsion angles in the final structure are printed out in the output (.dlg) file. The actual value of the torsion angle is defined relative to the starting torsion angle. For example, if you want the torsion to stay near where it is in the starting structure, you would set it to zero, and also set the dihe0 value to 0. instead of random in the .dpf file. Best regards, Maggie Margaret A. Johnson Dept. of Chemistry Simon Fraser University Burnaby, B.C. Canada V5A 1S6 Tel. (604) 291-5650 Fax. (604) 291-3765 E-mail: johnsont@sfu.ca From chemistry-request@server.ccl.net Thu Apr 11 17:11:10 2002 Received: from haney.hbond.com ([207.137.2.252]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3BLB8j24847 for ; Thu, 11 Apr 2002 17:11:09 -0400 Received: (from haney@localhost) by haney.hbond.com (8.9.3/8.9.3) id OAA02183; Thu, 11 Apr 2002 14:10:56 -0700 From: "Dr. David N. Haney" Message-Id: <200204112110.OAA02183@haney.hbond.com> Subject: Re: CCL:reduced protein models To: masakatsu_w@yahoo.com (Masakatsu Watanabe) Date: Thu, 11 Apr 2002 14:10:24 -0700 (PDT) Cc: CHEMISTRY@ccl.net In-Reply-To: from "Masakatsu Watanabe" at Apr 11, 2002 12:08:10 PM X-Mailer: ELM [version 2.5 PL5] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Masa: I am surprised that you did not mention the work of old Moldyn (now part of SBI): C.E. Padilla, H.E. Alper, D.N. Chin, M. Watanabe, V. Karlov, K.B. Blair, H.M. Chun, O. Becker, L. Caves, R. Nagle, M. Karplus, and D.N. Haney (2000) J. Comp. Chem., 21(3): 159-184 "A Substructured Modeling Approach for Long Time Molecular Dynamics Simulations" I think we worked together on some of this, but maybe I am mistaken. This work led to a program called MBOND which was sold by MSI. I do not know if it is still available. As you point out, the methods are not great, but I think this is partly because they are so difficult to use correctly. However, I think a researcher might make some valuable use of the techniques and move them forward. > Dear Jie, > > Tremendous efforts have recently been poured into > developing a coarse-grain potential for simulating and > investigating large biological molecular motions > characterized by the long time dynamics. Here are some > references that can help you: > > 1) Troyer et.al. utilize the simple point-per-residue > potential developed by Miyazawa & Jernigan to perform > the Langevin dynamics. (Check > http://www.cmpharm.ucsf.edu/~troyer/eccc/toc.html). > > 2) The other approaches are to simplify amino acid > residues by more than one interaction point; > > - The Head-Gordon & Brooks approach are described as > the Virtual body Dynamics (See Biopolymers, 31, p 77, > 1991). In their approach, however, the development of > electrostatic potential is not so simple. Therefore, > we took their representations of residues and > developed our unique potential by defining the pair > distribution function, described by Bahar et. al. (See > PROTEINS, 29, p292, 1997), from the selected protein > molecules. This develop potential was used in the > simulation. > > - Haliloglu and Bahar (See Proteins, 31, p271, 1998) > had also utilized their developed a coarse-grain > potential for their MD simulations. > > - The coarser representation of residue is done by > Herzyk and Hubbard (See PROTEINS, 17, p310, 1993). > They used their residue representations in the content > of NMR refinement, but their representation can be > utilized to develop unique potential for the dynamics > simulation. > > I myself involved some researches to utilize > coarse-grain potential. In my opinion, there are not > particularly outstanding coarse-grain potentials yet. > Which coarse-grain potential be used in your study > truly depends on what level of detail information you > want to gain from the simulation. You can also expand > the search from the reference presented here. > > Hopefully, this will help you a bit. > > Masa Watanabe -- ######### David N. Haney, Ph.D. ######### # Haney Associates Phone - 858-483-1197 # # 5455 Westknoll Dr. FAX - 858-483-1046 # # La Jolla, CA 92037 Email - haney@hbond.com # ################# ##################### From chemistry-request@server.ccl.net Thu Apr 11 17:45:36 2002 Received: from jilau1.Colorado.EDU ([128.138.140.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3BLjaj25324 for ; Thu, 11 Apr 2002 17:45:36 -0400 Received: from ixion.colorado.edu (ixion.Colorado.EDU [128.138.107.182]) by jilau1.Colorado.EDU (8.11.6/8.11.6/UnixOps+Hesiod) with ESMTP id g3BLjUM326326 for ; Thu, 11 Apr 2002 15:45:30 -0600 (MDT) Subject: In re CCL:G98: Massage and %Chk From: The Matt To: chemistry@ccl.net Content-Type: multipart/signed; micalg=pgp-sha1; protocol="application/pgp-signature"; boundary="=-p1s4QQoRYs//cdfOvtFi" X-Mailer: Ximian Evolution 1.0.3 (1.0.3-1) Date: 11 Apr 2002 15:45:30 -0600 Message-Id: <1018561530.25623.82.camel@ixion.colorado.edu> Mime-Version: 1.0 --=-p1s4QQoRYs//cdfOvtFi Content-Type: text/plain Content-Transfer-Encoding: quoted-printable Ladies and gentlemen, thank you for your replies about my questions with "one-file" BSSE. My conclusion is, while the suggestions of re-Massage-ing the Chlorine back to 17.0 were correct in constructing a one-file calculation, this leads to the wrong answer! The reason is a fault in using one input file and one .chk file. To wit: First Step (no ghost): 24 basis functions 72 primitive gaussians 20 alpha electrons 20 beta electrons Second Step (ghost Cl): The nuclear charge for atom 1 has been changed to Z=3D 0 0.000000 ... 24 basis functions 72 primitive gaussians 11 alpha electrons 11 beta electrons Third Step (ghost CO2, turn on Cl): The nuclear charge for atom 1 has been changed to Z=3D 17 17.000000 The nuclear charge for atom 2 has been changed to Z=3D 0 0.000000 The nuclear charge for atom 3 has been changed to Z=3D 0 0.000000 The nuclear charge for atom 4 has been changed to Z=3D 0 0.000000 ... Warning: center 1 has no basis functions! ... 15 basis functions 45 primitive gaussians <-----!!!!! 9 alpha electrons 9 beta electrons In using just one Checkfile, Gaussian imports *no* basis functions for Cl into the third step, since center 1 is read as a ghost "Bq".=20 Obviously, this leads to a nonsensical answer. The right way to do this is to separate out the jobs as Mr. Cuffe suggested: > This solution may not appeal to you, but it should work on a unix=20 > system. Run as 3 separate jobs in sequence. for the Cshell a=20 > command line like the following should do the trick > g98 job1; cp trial.chk trial1.chk; g98 job2; g98 job3;& > Where job3 references trial1.chk and job2 references the original=20 > trial.chk. Thank you all for your prompt help, and remember, sometimes the long way is the best way. Sincerely, Matt Thompson --=20 "And isn't sanity really just a one-trick pony, anyway? I mean, all you get is one trick, rational thinking, but when you're good and crazy, ooh ooh ooh, the sky's the limit!" -- The Tick TheMatt -- http://ucsub.colorado.edu/~thompsma/Home.html --=-p1s4QQoRYs//cdfOvtFi Content-Type: application/pgp-signature; name=signature.asc Content-Description: This is a digitally signed message part -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.6 (GNU/Linux) Comment: For info see http://www.gnupg.org iD8DBQA8tgP60XRaGMGO968RAkpOAJwKJqcxXxbJJf3o5v+BvWQJQCrwAQCffp6p J7wNeu7OHLtoHYp+zatHyPI= =1VTk -----END PGP SIGNATURE----- --=-p1s4QQoRYs//cdfOvtFi-- From chemistry-request@server.ccl.net Thu Apr 11 17:54:04 2002 Received: from prserv.net ([32.97.166.34]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3BLs3j25474 for ; Thu, 11 Apr 2002 17:54:03 -0400 Received: from attglobal.net (slip-32-101-203-51.in.us.prserv.net[32.101.203.51]) by prserv.net (out4) with SMTP id <2002041121535020406jk820e>; Thu, 11 Apr 2002 21:53:51 +0000 Message-ID: <3CB5BF5E.3456DB9A@attglobal.net> Date: Thu, 11 Apr 2002 16:52:47 +0000 From: jmmckel@attglobal.net Reply-To: jmmckel@attglobal.net X-Mailer: Mozilla 4.79 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: Johannes Weber CC: chemistry@ccl.net Subject: Re: CCL:SUMMARY: g98: TD-DFT geometry optimizations ? References: Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Keep ypur eyes out for TDDFT gradients in Q-Chem and Turbomole in the not too distant future, rumors have it. John McKelvey Johannes Weber wrote: > Dear CCL members, > > Two weeks ago I posted a g98 related question concerning geometry > optimizations and frequency calculations with the time-dependent DFT > method. Here is the original question: > ------------------------------------------------------------- > Dear CCL members, > > I have a Gaussian 98 related question: > > According to the g98 users manual (p. 155, TD keyword) it should be > possible to do Time Dependent DFT geometry optimizations of the N-th > excited state using the Root=N option. > > However, I can´t find a proper input. The easiest input line > > #P TD=(Root=1) B3LYP/STO-3G Test DENSITY OPT=Z-Matrix > > leads to an error in link 1002: > > (Enter /vol/chemie/libexec/g98.A9/g98/l1002.exe) > Minotr: Closed-shell wavefunction. > Cannot mix post-SCF and DFT. > Error termination via Lnk1e in /vol/chemie/libexec/g98.A9/g98/l1002.exe. > > I played around with several other options, tried to do the job in a two > step procedure, like it is described for the CIS method in > Forsman/Frisch´s "Exploring Chemistry with Electronic Structure Methods", > all without success. Is it possible to do these calculations? Anybody out > there with experience in this topic? The ultimate goal would be to perform > a normal mode frequency calculation for excited states within the TD-DFT > formalism. > > Regards, :-)ohannes. > --------------------------------------------------------------------- > > I got several answers, my special thanks go to Dr. Doug Fox and Prof. > Galina Orlova for the fruitful discussion. Other people which I´m indebted > to are Wolfgang Roth and Rainer Remenyi. To put it in a nutshell: > > Yes, you can do TDDFT geometry optimizations and frequency calculations. > However, since no gradients and higher derivatives are available for this > method in g98, you have to resort to numerical optimizations, namely using > the EF-algorithm with the opt=(Enonly,Z-Matrix) and freq=(Enonly) > keyword. The optimization has to be performed in Z-Matrix coordinates > and you need an initial guess for the force constants, which Dr. Fox > recommended to take from a CIS calculation (optimization and frequency > calculation). You can also try an take the force constants out of a > different calculation with the RCFC option in the opt keyword. Opt and > freq calculation have to be done in subsequent steps, a one-step procedure > with opt and freq in the same input card will fail. > > To my (very limited) experience the usability of TDDFT optimizations is > restricted by the fact that the numerical derivatives suffer from long run > times (especially the freq calculations are really expensive for > polyatomic molecules!) and a quite low accuracy (this is at least what I > found from in the calculated frequencies). Until now, I wasn´t able to > use force constants from other than CIS calculations for the initial > guess. > > Best regards and thanks again to all people who answered. The relevant > original answers are appended below. > > :-)ohannes. > > ====================================================================== > answer 1: > From: Doug Fox > Subject: Re: CCL:g98: TD-DFT geometry optimizations ? > > Dr Weber, > > The manual is in error and there is not an implementation of > analytic gradients for TD-DFT nor is there for TD-HF (aka RPA). > > You can get various roots and if you use OPT=(RCFC,EnOnly), taking the > force constants perhaps from a single point CIS FREQ calculation, you > could do a geometry optimization. Note that this will be more practical > for smaller systems. > ====================================================================== > > answer 2: Prof Orlova forwarded an email to me that she had received > earlier from Jim Hess, help@gaussian.com. > > From: Galina Orlova > Subject: Fwd: Re: TDDFT (from WWW) > > ----- Forwarded message from gaussian.com!help@gaussian.com ----- > Date: Mon, 25 Mar 2002 11:49:06 -0500 > From: gaussian.com!help@gaussian.com > Reply-To: gaussian.com!help@gaussian.com > Subject: Re: TDDFT (from WWW) > To: gorlova@uoguelph.ca > > Dear Galina, > Since there aren't analytic gradients available for TD methods, > normal geometry optimizations are not possible with this keyword. The > error you get with TD-DFT occurs when Gaussian actually tries to > calculate the analytic gradient, but fails to find the necessary data. > The only way to do a td-dft optimization is with numerical gradients. To > > do this, use "opt=(enonly,rcfc)". This option requires that the > optimization be done in symbolic z-matrix coordinates and that initial > force constants be read from the checkpoint file or from cards. The > force constants would typically come from an analytic frequency. In this > > case, CIS frequencies seem to be the logical choice. As for your TD-HF > optimizations, I'm afraid to say that they are not truly TD-HF > optimizations. The code should give an error message, but instead it > does the optimization using something very close to a CIS gradient. > Since the optimizations you already completed were done with gradients > based upon CIS, if you choose to go ahead with the numerical TD-HF > geometry optimizations, these final geometries should be fairly close to > > the TD-HF minimum so I'd recommend using them as initial structures. > > Regards, > Jim Hess > --------------------------------------------------------------------- > >... > Dr. Galina Orlova > Vis. Res. Professor > Department of Chemistry and Biochemistry > University of Guelph > Guelph, ON, Canada N1G 2W1 > tel. work (Int+1)(519)824-4120 ext 3102 > home (Int+1)(519)829-3119 > fax (519)766-1499 > e-mail gorlova@uoguelph.ca > ===================================================================== > > answer 3: > From: Wolfgang Roth > Subject: Re: CCL:g98: TD-DFT geometry optimizations ? > > Hallo Johannes, > > ich habe zwar schon eine ganze Weile nichts mehr mit Gaussian gerechnet > und kenne auch die neuesten Features nicht, ABER: > > Zu dem von Dir beschriebenen Problem > >According to the g98 users manual (p. 155, TD keyword) it should be > >possible to do Time Dependent DFT geometry optimizations of the N-th > >excited state using the Root=N option. > kann ich Dir folgendes sagen: > Der TD-DFT output von G98 Rev a.7 und a.9 sieht genauso aus wie die > AUsgabe, die man bei einer CIS-Rechnung bekommt. Deswegen gehe ich mal > davon aus, daß die Programmierer die Algorithmen wiederverwendet haben. > Das "Root" Keyword beschreibt nur den "state of interest" d.h. den > gewünchten elektronischen Zustand, für den die gewählte Rechnung > durchzuführen ist. Ob man oder ob man nicht Geometrieoptimierungen > durchführen kann ist bei der Berechnung der Wellenfunktion nicht von > belang. Meines Wissens gibt es in keinem Programm einen Algorithmus zur > Geometrieoptimierung mit Time dependent Methoden, auch nicht für TD-HF, > das > ja eigentlich der CIS-Methode sehr ähnlich/vergleichbar sein sollte. > Das Problem ist, daß es wohl keine Gradienten für den TD (EOM??) > Algorithmus gibt. > > > Is it possible to do these calculations? > Ich denke: NEIN > ich habs auch mal über die numerische Gradienten versucht, da tut Gaussian > dann ywar ne ganze Weile (3N TD-DFT single points lang) was, steigt dann > aber mit Fehlermeldung/ohne Ergebnis aus. > > >Anybody out there with experience in this topic? The ultimate goal would > be to perform > >a normal mode frequency calculation for excited states within the TD-DFT > >formalism. > Ja, das wär wirklich nett, v.a. weil CASSCF Freqs mit Gaussian mühsam > sind.. > > Schöne Grüße > Wolfgang > > ==W=R===========================W=o=l=f=g=a=n=g==R=o=t=h== > TU Brauschweig > Institut f. Physikalische und Theoretische Chemie > Hans-Sommer-Strasse 10 Tel ++49 (0)531 391 5346 > 38106 Braunschweig Fax ++49 (0)531 391 5396 > ======== http://www-public.tu-bs.de:8080/~wroth/ ========= > > ===================================================================== > > answer 4: > > From: Rainer Remenyi > Subject: Re: CCL:g98: TD-DFT geometry optimizations ? > > Hi Johannes, > > Try UB3LYP instead of B3LYP. > > Regards, > > Rainer Remenyi > Universität Heidelberg > ===================================================================== > > answer 5: The second answer of Prof. Orlova, after I asked her if she also > calculated the frequencies. > > Hi, Johannes > > I guess, if G98 does not have analitic gradients for TD then it does not > have analitic second deriv. either. So you must run frequencies > numerically (freq=numer). If you did do so and it still doesn't work you > better ask the gaussian helpers. Unfortunately, my systems are so large > that even numerical optimization is a great problem. Thus I don't have > experience with numerical frequencies within TDDFT. > > Jim means the TD-hartree-Fock (not TDDFT!) optimization I've run > "successfully" analitically. In fact, G98 must abort this job. For some > reason it was running but Jim's guess is that in fact G98 performed the > CIS-HF optimization instead of TD-HF. Actually,the CIS-HF results might be > very close to those from TD-HF optimization with numerical derivatives. > > best regards, Galina > > Dr. Galina Orlova > Vis. Res. Professor > Department of Chemistry and Biochemistry > University of Guelph > Guelph, ON, Canada N1G 2W1 > tel. work (Int+1)(519)824-4120 ext 3102 > home (Int+1)(519)829-3119 > fax (519)766-1499 > e-mail gorlova@uoguelph.ca > ======================================================================== > > answer 6: The second answer of Dr. Fox, after I tried out a numerical > frequency optimization -- with peculiar results. > > From: "Cust. Service Doug" > Subject: Re: CCL:g98: TD-DFT geometry optimizations ? > > Dr. Weber, > > There is no option to do numerical or enonly frequencies as a > part of an optimization. > >... > As to your first point clearly the attempt a multi-step job, ie. OPT > FREQ, is generating a bad keyword. As this is still present in the > current revision I can only suggest you do this as a two step job, > OPT=(RCFC,Enonly) as the first and then FREQ=Enonly for the second. > I will have the combination examined for a future release but we don't > plan any further bug fixes for G98 at this point. Note that it has > created the bad combination RTD-B3LYP. It may also have a problem > with correctly generating FREQ=EnOnly but I can't confirm that because > it fails before actually generating that route. > > Numerical frequencies do suffer from much lower precision. The > step size is a compromise between the infinitesmal step which > would be the closes approximation to the analytic derivative but > which has such a small energy difference that it is numerically > inaccurate or a larger step which gives a numerically stable > energy difference but might step outside of the harmonic region > and introduce errors that way. In the case of very low frequencies > you are probably better off using a somewhat larger step as the > low frequencies will require a larger step to get a significant > energy difference. Smaller steps might help the higher frequencies > but that is less important for the optimization. > >... > > > > > Dear Dr. Fox,=20 > > > > thanks again for your quick response. After the easter vacation I now > > come back to the TDDFT geometry optimization and frequency calculation > > problem and pester you with further questions. Please, be patient with > me!= > > =20 > > :-) I tested several cases with a minimal basis on para-benzoquinone. > My > > results are as follows:=20 > > > > (1) I managed to do a numerical frequency calculation after the > > optimization job. However, it seems not possible to do a geometry > > optimization and a frequency calculation in a single step! Having done a > > CIS-optimization and freq calculation in advance the input card > > > > > # TD=3D(Root=3D1,Read) RB3LYP/STO-3G INTEGRAL(GRID=3DULTRAFINE) Test > > > DENSITY=3Dcurrent Geom=3DCheck Guess=3DRead OPt=3D(EnOnly,RCFC) > Freq=3DEN= > > Only =20 > > > > leads - after a sucessful TD-DFT geometry optimization - to the > following > > error message in the freq run: > > > > >... > > > ------------------------------------------------------------ > > > #P Geom=3DAllCheck Guess=3DTCheck Test RTD-B3LYP(FC)/STO-3G Freq > > > ------------------------------------------------------------ > > > QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT LINE. > > > GUESS=3DTCHECK TEST RTD-B3LYP(FC)/STO-3G=20 > > > ' > > > Last state=3D"GCL" > > > TCursr=3D 820 LCursr=3D 44 > > > Error termination via Lnk1e in /vol/chemie/libexec/g98.A9/g98/l1.exe. > > > Job cpu time: 0 days 0 hours 0 minutes 0.1 seconds. > > > File lengths (MBytes): RWF=3D 105 Int=3D 0 D2E=3D 0 Chk=3D > 12 S= > > cr=3D1 > > > Segmentation Fault > > >... > > > > In contrast, the following two step procedure seems to work: > > > > > %chk=3Dpbq.chk > > > # TD=3D(Root=3D1,Read) RB3LYP/STO-3G INTEGRAL(GRID=3DULTRAFINE) Test > > > DENSITY=3Dall Geom=3DAllcheck Guess=3DRead OPt=3D(EnOnly,RCFC)=20 > > > > > > > > Why is this the case? Does the single step procedure always assume > > analytical frequencies, even though Freq=3DENOnly was specified > originally?= > > =20 > >... > ====================================================================== > > ---------------------------------------------------------------------- > | Johannes Weber | Email: | > | Universitaet zu Koeln | Johannes.Weber@uni-koeln.de | > | Institut fuer Physikalische Chemie | | > | Lehrstuhl Prof. Dr. G. Hohlneicher | tel: 0049-(0)221-470-4812 | > | Luxemburger Str. 116 | fax: 0049-(0)221-470-5144 | > | 50939 Koeln | | > ---------------------------------------------------------------------- > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Fri Apr 12 04:07:32 2002 Received: from ciril.fr ([193.50.27.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3C87Uj05292 for ; Fri, 12 Apr 2002 04:07:31 -0400 Received: from host20.lctn.uhp-nancy.fr (host20.lctn.uhp-nancy.fr [193.50.239.24]) by ciril.fr (8.12.3/8.12.3/Guy-23-01-2002) with ESMTP id g3C87NT0000679; Fri, 12 Apr 2002 10:07:23 +0200 (METDST) Received: from lctn.uhp-nancy.fr (host23.lctn.uhp-nancy.fr [193.50.239.30]) by host20.lctn.uhp-nancy.fr (AIX4.3/8.9.3/8.9.3) with ESMTP id KAA22224; Fri, 12 Apr 2002 10:08:50 +0200 Sender: assfeld@host20.lctn.uhp-nancy.fr Message-ID: <3CB6931C.6873C9C2@lctn.uhp-nancy.fr> Date: Fri, 12 Apr 2002 09:56:12 +0200 From: Xavier ASSFELD Organization: Chimie Theorique X-Mailer: Mozilla 4.51i [en] (X11; I; AIX 4.3) X-Accept-Language: en MIME-Version: 1.0 To: The Matt , CCL Subject: Re: CCL:In re G98: Massage and %Chk References: <1018561530.25623.82.camel@ixion.colorado.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Virus-Scanned: by amavisd-milter arcturus (http://amavis.org/) Hello, I think it is possible to have only one input file using the CHKBAS keyword. Here follows a silly exemple: %CHK=hene.chk # RHF/STO-3G SCF=(DIRECT,TIGHT) He...Ne 0 1 He Ne 1 3.0 --LINK1-- %CHK=hene.chk # RHF/CHKBAS SCF=(TIGHT,DIRECT) GUESS=CHECK GEOM=ALLCHECK MASSAGE 1 NUC 0.0 --LINK1-- %CHK=hene.chk # RHF/CHKBAS SCF=(TIGHT,DIRECT) GUESS=CHECK GEOM=ALLCHECK MASSAGE 1 NUC 2.0 2 NUC 0.0 Hope this helps. -- ...Xav Ast. Pr. Xavier Assfeld Xavier.Assfeld@lctn.uhp-nancy.fr Laboratoire de Chimie theorique (T) 33 3 83 91 21 49 Universite Henri Poincare (F) 33 3 83 91 25 30 F-54506 Nancy BP 239 http://www.lctn.uhp-nancy.fr From chemistry-request@server.ccl.net Fri Apr 12 07:28:40 2002 Received: from ciril.fr ([193.50.27.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3CBSdj09748 for ; Fri, 12 Apr 2002 07:28:40 -0400 Received: from host20.lctn.uhp-nancy.fr (host20.lctn.uhp-nancy.fr [193.50.239.24]) by ciril.fr (8.12.3/8.12.3/Guy-23-01-2002) with ESMTP id g3C7qAT0027037; Fri, 12 Apr 2002 09:52:11 +0200 (METDST) Received: from lctn.uhp-nancy.fr (host23.lctn.uhp-nancy.fr [193.50.239.30]) by host20.lctn.uhp-nancy.fr (AIX4.3/8.9.3/8.9.3) with ESMTP id JAA16430; Fri, 12 Apr 2002 09:53:38 +0200 Sender: assfeld@host20.lctn.uhp-nancy.fr Message-ID: <3CB68F8C.FB09701E@lctn.uhp-nancy.fr> Date: Fri, 12 Apr 2002 09:41:00 +0200 From: Xavier ASSFELD Organization: Chimie Theorique X-Mailer: Mozilla 4.51i [en] (X11; I; AIX 4.3) X-Accept-Language: en MIME-Version: 1.0 To: Zhen Xie , CCL Subject: Re: CCL:Re: about PES scan References: <200204111458.WAA24867@mx1.ustc.edu.cn> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Virus-Scanned: by amavisd-milter arcturus (http://amavis.org/) Hello, You have too much variables for what you wanna do. Since you optimize the geometry at each step, you will end at the same final structure 600 times! If you want to scan the CC distance in C2H2, you need to freeze variable. In fact the only variable that needs to be optimized is the CH bond distance. You could try this input file: #p uhf/6-311g** opt=z-matrix nosymm pes scan yique 0.2-0.002 0 1 X X 1 xx C 1 cx1 2 acx1 C 2 cx2 1 acx2 3 da1 H 3 ch1 1 ach1 2 da2 H 4 ch1 2 ach2 1 da3 xx 0.5 S 600 0.002 ch1=1.0 cx1=2.0 cx2=2.0 acx1=90. acx2=90. ach1=90. ach2=90. da1=0. da2=180. da3=180. Hope this helps. -- ...Xav Ast. Pr. Xavier Assfeld Xavier.Assfeld@lctn.uhp-nancy.fr Laboratoire de Chimie theorique (T) 33 3 83 91 21 49 Universite Henri Poincare (F) 33 3 83 91 25 30 F-54506 Nancy BP 239 http://www.lctn.uhp-nancy.fr From chemistry-request@server.ccl.net Fri Apr 12 04:44:21 2002 Received: from cefni.aber.ac.uk ([144.124.16.40]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3C8iLj06063 for ; Fri, 12 Apr 2002 04:44:21 -0400 Received: from margaux.dcs.aber.ac.uk ([193.60.10.14] helo=aber.ac.uk) by cefni.aber.ac.uk with esmtp (Exim 3.21 #1) id 16vwfA-0000zL-00; Fri, 12 Apr 2002 09:44:08 +0100 Sender: dle@aber.ac.uk Message-ID: <3CB69E85.7D538560@aber.ac.uk> Date: Fri, 12 Apr 2002 09:44:53 +0100 From: David Enot X-Mailer: Mozilla 4.61C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: quch quch CC: chemistry@ccl.net Subject: Re: CCL:standard dataset for docking. References: <20020411200933.79038.qmail@web13402.mail.yahoo.com> Content-Type: multipart/alternative; boundary="------------34043F27AFCAE1C46DAAFA57" --------------34043F27AFCAE1C46DAAFA57 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, You could have a look to that paper : Bissantz, Folkers & Rognan, J Med Chem, 2000, 43, 4759-4767. There is a comparison between scoring function and docking programs for 2 proteins. Best regards, David -- ********************* David P. Enot, Ph D. *********************** * Department of Computer Science Work : +44 1970 622357 * * Computational Biology Group Fax : +44 1970 622455 * * U.W.A. - Aberystwyth SY23 3DB, UK Mobile : +44 7779 030629 * ********************* Email : dle@aber.ac.uk ********************* --------------34043F27AFCAE1C46DAAFA57 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit  
    Hi,

    You could have a look to that paper :

                Bissantz, Folkers & Rognan, J Med Chem, 2000, 43, 4759-4767.

    There is a comparison between scoring function and docking programs for 2 proteins.

    Best regards,

            David
  

-- 
 *********************  David P. Enot, Ph D.  ***********************
 *  Department of Computer Science        Work   : +44 1970 622357  *
 *  Computational Biology Group           Fax    : +44 1970 622455  *
 *  U.W.A. - Aberystwyth SY23 3DB, UK     Mobile : +44 7779 030629  *
 *********************  Email : dle@aber.ac.uk  *********************
  --------------34043F27AFCAE1C46DAAFA57-- From chemistry-request@server.ccl.net Fri Apr 12 04:11:21 2002 Received: from ribotargets.com ([194.129.39.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3C8BKj05379 for ; Fri, 12 Apr 2002 04:11:20 -0400 Received: from szilva (helo=localhost) by echo.ribotargets.com with local-esmtp (Exim 3.13 #1) id 16vw5a-0002lH-00; Fri, 12 Apr 2002 08:07:22 +0000 Date: Fri, 12 Apr 2002 08:07:22 +0000 (GMT) From: Szilveszter Juhos To: quch quch cc: chemistry@ccl.net Subject: Re: CCL:standard dataset for docking. In-Reply-To: <20020411200933.79038.qmail@web13402.mail.yahoo.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 11 Apr 2002, quch quch wrote: > Is there any standard (or acceptable) docked datasets > available for comparing different score functions? There is no standard set. De facto sets are the GOLD and FlexX (partly overlapping). Also worth to give a try with spiked libs (check at http://www.schrodinger.com/Documents/GlideDataSheet.doc ) Cheers: Szilva From chemistry-request@server.ccl.net Fri Apr 12 03:32:34 2002 Received: from mx3.ust.hk ([143.89.13.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3C7WXj03835 for ; Fri, 12 Apr 2002 03:32:33 -0400 Received: from chz122 (chz122.ust.hk [143.89.53.117]) by mx3.ust.hk (8.12.2/8.12.2) with ESMTP id g3C7WLRp078224 for ; Fri, 12 Apr 2002 15:32:22 +0800 (HKT) Message-ID: <00df01c1e1f3$bf1aed40$7535598f@ust.hk> From: "Chungen(IMAP.ust.hk)" To: Subject: About the solvent effect calculation. Date: Fri, 12 Apr 2002 15:29:13 +0800 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_00DC_01C1E236.CC9F7C40" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 This is a multi-part message in MIME format. ------=_NextPart_000_00DC_01C1E236.CC9F7C40 Content-Type: text/plain; charset="gb2312" Content-Transfer-Encoding: quoted-printable Dear ccler I am confused with the PCM calculations. The system is a bit too = large, about 60 heavy atoms, and the basis number is about 1000.=20 =20 The keyword looks like: #P HF/3-21G scrf=3D(pcm,solvent=3D2) scf=3Ddirect Error message looks like: Too many tesserae. Increase the MxTs. Error termination via Lnk1e in /usr/local/g98/l502.exe. Anyone can give me advices on solving this problem? Best regards Chungen ------=_NextPart_000_00DC_01C1E236.CC9F7C40 Content-Type: text/html; charset="gb2312" Content-Transfer-Encoding: quoted-printable
Dear ccler
 
I am confused with the PCM = calculations.  The=20 system is a bit  too large, about 60 heavy atoms, and the basis = number is=20 about 1000.
 
The keyword looks like:
 
 
#P HF/3-21G scrf=3D(pcm,solvent=3D2)=20 scf=3Ddirect
 
 
Error message looks like:
 

 Too many tesserae.  = Increase the=20 MxTs.
 Error termination via Lnk1e in=20 /usr/local/g98/l502.exe.
 
Anyone can give me advices on solving = this=20 problem?
 
Best regards
 
Chungen
 
------=_NextPart_000_00DC_01C1E236.CC9F7C40-- From chemistry-request@server.ccl.net Fri Apr 12 09:03:18 2002 Received: from jeeves.ccdc.cam.ac.uk ([131.111.113.44]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3CD3Hj12063 for ; Fri, 12 Apr 2002 09:03:17 -0400 Received: from odin.ccdc.cam.ac.uk ([131.111.113.134] helo=ccdc.cam.ac.uk) by jeeves.ccdc.cam.ac.uk with esmtp (Exim 3.12 #1 (Debian)) id 16w0hr-0007hI-00; Fri, 12 Apr 2002 14:03:11 +0100 Sender: cole@ccl.net Message-ID: <3CB6DB0E.6FBAAA0E@ccdc.cam.ac.uk> Date: Fri, 12 Apr 2002 14:03:10 +0100 From: Jason Cole Organization: CCDC X-Mailer: Mozilla 4.07C-SGI [en] (X11; I; IRIX 6.5 IP32) MIME-Version: 1.0 To: quch quch CC: chemistry@ccl.net Subject: Re: CCL:standard dataset for docking. References: <20020411200933.79038.qmail@web13402.mail.yahoo.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Should have sent this into the site; originally only sent it to quch quch The gold test set is freely available at http://www.ccdc.cam.ac.uk/prods/gold/value.html just grab the tar.gz file on the pages. If you use it and publish anything then please add in a reference to the original GOLD paper, or to the CCDC. My colleague, Willem Nissink, and co-workers have also recently submitted a paper containing 300 or so systems which merge the ChemScore set, GoldScore set and also add a further 100 or so complexes; this will eventually become freely available too. If anyone fancies looking up affinity data for these systems it would be very welcome :) Jason From chemistry-request@server.ccl.net Fri Apr 12 10:22:08 2002 Received: from jilau1.Colorado.EDU ([128.138.140.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3CEM8j14030 for ; Fri, 12 Apr 2002 10:22:08 -0400 Received: from ixion.colorado.edu (ixion.Colorado.EDU [128.138.107.182]) by jilau1.Colorado.EDU (8.11.6/8.11.6/UnixOps+Hesiod) with ESMTP id g3CEKkM469872; Fri, 12 Apr 2002 08:20:46 -0600 (MDT) Subject: Re: CCL:In re G98: Massage and %Chk From: The Matt To: Xavier ASSFELD Cc: CCL List In-Reply-To: <3CB6931C.6873C9C2@lctn.uhp-nancy.fr> References: <1018561530.25623.82.camel@ixion.colorado.edu> <3CB6931C.6873C9C2@lctn.uhp-nancy.fr> Content-Type: multipart/signed; micalg=pgp-sha1; protocol="application/pgp-signature"; boundary="=-JgL78cdwYtIKN1Sfs+T6" X-Mailer: Ximian Evolution 1.0.3 (1.0.3-1) Date: 12 Apr 2002 08:20:46 -0600 Message-Id: <1018621246.30081.8.camel@ixion.colorado.edu> Mime-Version: 1.0 --=-JgL78cdwYtIKN1Sfs+T6 Content-Type: text/plain Content-Transfer-Encoding: quoted-printable On Fri, 2002-04-12 at 01:56, Xavier ASSFELD wrote: > Hello, >=20 > I think it is possible to have only one input file > using the CHKBAS keyword. > Here follows a silly exemple: >=20 > %CHK=3Dhene.chk > # RHF/STO-3G SCF=3D(DIRECT,TIGHT) >=20 > He...Ne >=20 > 0 1 > He > Ne 1 3.0 >=20 > --LINK1-- > %CHK=3Dhene.chk > # RHF/CHKBAS SCF=3D(TIGHT,DIRECT) GUESS=3DCHECK GEOM=3DALLCHECK MASSAGE >=20 > 1 NUC 0.0 >=20 > --LINK1-- > %CHK=3Dhene.chk > # RHF/CHKBAS SCF=3D(TIGHT,DIRECT) GUESS=3DCHECK GEOM=3DALLCHECK MASSAGE >=20 > 1 NUC 2.0 > 2 NUC 0.0 You are quite right, it does work. Thank you for pointing out this option, it's new to me and useful. It will make life easier (much fewer files to handle). Matt Thompson --=20 "And isn't sanity really just a one-trick pony, anyway? I mean, all you get is one trick, rational thinking, but when you're good and crazy, ooh ooh ooh, the sky's the limit!" -- The Tick TheMatt -- http://ucsub.colorado.edu/~thompsma/Home.html --=-JgL78cdwYtIKN1Sfs+T6 Content-Type: application/pgp-signature; name=signature.asc Content-Description: This is a digitally signed message part -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.6 (GNU/Linux) Comment: For info see http://www.gnupg.org iD8DBQA8tu0+0XRaGMGO968RAt/NAJ91VA65VxYKtlrk5HyYkI9+aJX1MgCfUn87 K9HaYyjIsZt6MVqbwV20G0c= =qNaq -----END PGP SIGNATURE----- --=-JgL78cdwYtIKN1Sfs+T6-- From chemistry-request@server.ccl.net Fri Apr 12 10:49:01 2002 Received: from sun1.udg.es ([130.206.45.89]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3CEn1j14677 for ; Fri, 12 Apr 2002 10:49:01 -0400 Received: from iqc.udg.es (woodstock.udg.es [130.206.128.118]) by sun1.udg.es (8.9.3/8.9.3/otb) with ESMTP id QAA15238 for ; Fri, 12 Apr 2002 16:47:51 +0100 (WET DST) Message-ID: <3CB710A0.5080408@iqc.udg.es> Date: Fri, 12 Apr 2002 18:51:44 +0200 From: Pedro Salvador Sedano User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:0.9.4.1) Gecko/20020314 Netscape6/6.2.2 X-Accept-Language: en-us MIME-Version: 1.0 CC: CCL Subject: Re: CCL:In re G98: Massage and %Chk References: <1018561530.25623.82.camel@ixion.colorado.edu> <3CB6931C.6873C9C2@lctn.uhp-nancy.fr> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hello, I'd like to add that it's not a good option to use as a guess for the ghost orbital calculations the MO obtained in the dimer calculation, as at least one of the first two molecular orbitals would lay on the ghost functions, which is a very bad choice... Xavier ASSFELD wrote: > Hello, > > I think it is possible to have only one input file > using the CHKBAS keyword. > Here follows a silly exemple: > > %CHK=hene.chk > # RHF/STO-3G SCF=(DIRECT,TIGHT) > > He...Ne > > 0 1 > He > Ne 1 3.0 > > --LINK1-- > %CHK=hene.chk > # RHF/CHKBAS SCF=(TIGHT,DIRECT) GUESS=CHECK GEOM=ALLCHECK MASSAGE > > 1 NUC 0.0 > > --LINK1-- > %CHK=hene.chk > # RHF/CHKBAS SCF=(TIGHT,DIRECT) GUESS=CHECK GEOM=ALLCHECK MASSAGE > > 1 NUC 2.0 > 2 NUC 0.0 > > > Hope this helps. > -- -------------------------------------------------------------------- Pedro Salvador Sedano Ph.D. Student I'll stare the sundown, Institut de Quimica Computacional untill my eyes go blind. Universitat de Girona I won't change direction, Campus Montilivi 17071, Girona,Spain and I won't change my mind. iqc.udg.es/~perico -------------------------------------------------------------------- From chemistry-request@server.ccl.net Fri Apr 12 17:41:21 2002 Received: from umbi3.umbi.umd.edu ([136.160.7.51]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3CLfLj22189 for ; Fri, 12 Apr 2002 17:41:21 -0400 Received: from umbi.umd.edu ([129.6.113.76]) by umbi3.umbi.umd.edu (Netscape Messaging Server 4.15) with ESMTP id GUH5M600.MKU for ; Fri, 12 Apr 2002 17:42:06 -0400 Message-ID: <3CB754AA.539EA14F@umbi.umd.edu> Date: Fri, 12 Apr 2002 17:42:03 -0400 From: "Michael K. Gilson" X-Mailer: Mozilla 4.78 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: New Data at BindingDB Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear Colleagues, The Binding Database (www.bindingdb.org) now includes nearly 170 measured affinities of HIV-1 protease for cyclic urea inhibitors, measured by enzyme inhibition.* This series should be particularly useful for parameterizing and testing computational models of binding because the measurements were all done with the same assay and the inhibitors are all expected to have a similar binding mode. You can find these data by typing "HIV" into the search bar at www.bindingdb.org. If you want an MDL Molfile for an entry, click "more" in the corresponding line of the data table and use the JChem applet at the bottom of the page. (In JChem, use "Edit"--> "Source".) The PDB contains several structures that illustrate the binding mode. (Search the PDB for "cyclic urea".) Examples include 1dmp and 1hvr. We hope you will find these binding data interesting and useful. Please let me know of any problems you may have accessing them. If you have binding data in electronic form that could be published at BindingDB-- for example, data already published in J. Med. Chem. -- we would be happy to include them in BindingDB, so please send them along. This is a good way to help BindingDB grow. Finally, please let me know if there are any specific classes of data (e.g., kinase binding) you think BindingDB should try to collect and make available on-line. With best regards, Mike Gilson Center for Advanced Research in Biotechnology University of Maryland Biotechnology Insitute * Thanks to the DuPont Merck Pharmaceutical Company for providing these data in electronic format several years ago. From chemistry-request@server.ccl.net Fri Apr 12 12:41:08 2002 Received: from dagger.nd.edu ([129.74.250.101]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3CGf8j16401 for ; Fri, 12 Apr 2002 12:41:08 -0400 Received: from mshield (shield2.cc.nd.edu [129.74.250.49]) by dagger.nd.edu (8.12.2/8.12.2) with SMTP id g3CGf3tY013582 for ; Fri, 12 Apr 2002 11:41:03 -0500 (EST) Received: FROM vivaldi BY mshield ; Fri Apr 12 11:38:13 2002 -0500 Message-ID: <003301c1e240$d6373090$3f504a81@vivaldi> From: "Patrick Laine" To: Subject: Macromodel: error generating interactions Date: Fri, 12 Apr 2002 11:41:04 -0500 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0030_01C1E216.ED5C6DA0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4807.1700 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 This is a multi-part message in MIME format. ------=_NextPart_000_0030_01C1E216.ED5C6DA0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable I am trying to submit a conformational search(Monte Carlo) using = macromodel and the amber force field and the job will not run because = when the program tries to load the parameters from the force field I get = a message saying: INTFFC: No nonbonded params in force field for atom type 17 (OA) INTFFC: No nonbonded params in force field for atom type 29 (NC) INTFFC: No nonbonded params in force field for atom type 33 (NE) INTFFC: No nonbonded params in force field for atom type 34 (NF) INTFFC: No nonbonded params in force field for atom type 35 (NG) UPDATE_INT: INTFFC fails Monitored BatchMin job completed. Error generating interactions; see LOG file When I view the force field and all of the nonbonded params within, I = find no problem. I look for those specific atoms listed above, and I = can still not find the problem. I have tried to redraw those atoms in = macromodel, but that doesn't work either. Your help would be greatly appreciated, Thank you, Patrick Laine Graduate Student University of Notre Dame Department of Chemistry and Biochemistry 372 Stepan Hall=20 Work: 574-631-4007 ------=_NextPart_000_0030_01C1E216.ED5C6DA0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
I am trying to submit a conformational = search(Monte=20 Carlo) using macromodel and the amber force field and the job will not = run=20 because when the program tries to load the parameters from the force = field I get=20 a message saying:
INTFFC: No nonbonded params in force = field for atom=20 type  17 (OA)
INTFFC: No nonbonded params in force = field for atom=20 type  29 (NC)
INTFFC: No nonbonded params in force = field for atom=20 type  33 (NE)
INTFFC: No nonbonded params in force = field for atom=20 type  34 (NF)
INTFFC: No nonbonded params in force = field for atom=20 type  35 (NG)
UPDATE_INT:  INTFFC fails
Monitored BatchMin job completed.
Error generating interactions; see LOG file
 
When I view the force field and all of the nonbonded params within, = I find=20 no problem.  I look for those specific atoms listed above, and I = can still=20 not find the problem.  I have tried to redraw those atoms in = macromodel,=20 but that doesn't work either.
 
Your help would be greatly appreciated,
Thank you,
 
Patrick Laine
Graduate = Student
University of=20 Notre Dame
Department of Chemistry and Biochemistry
372 Stepan = Hall=20
Work:  574-631-4007
------=_NextPart_000_0030_01C1E216.ED5C6DA0-- From chemistry-request@server.ccl.net Fri Apr 12 14:15:41 2002 Received: from mxout1.cac.washington.edu ([140.142.32.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3CIFfj17881 for ; Fri, 12 Apr 2002 14:15:41 -0400 Received: from mailscan-out3.cac.washington.edu (mailscan-out3.cac.washington.edu [140.142.32.18]) by mxout1.cac.washington.edu (8.12.1+UW01.12/8.12.1+UW02.01) with SMTP id g3CIFVYB030029 for ; Fri, 12 Apr 2002 11:15:31 -0700 Received: FROM dante58.u.washington.edu BY mailscan-out3.cac.washington.edu ; Fri Apr 12 11:15:31 2002 -0700 Received: from localhost (jzheng73@localhost) by dante58.u.washington.edu (8.12.1+UW01.12/8.12.1+UW02.01) with ESMTP id g3CIFV4b125100 for ; Fri, 12 Apr 2002 11:15:31 -0700 Date: Fri, 12 Apr 2002 11:15:30 -0700 (PDT) From: "J. Zheng" To: chemistry@ccl.net Subject: Summary: Reduced Protein Models Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLer: > > I have a general question about the protein simulation. For protein > > simulation, force field is important issue. As I know as far, most of > > persons use different force fields such as Charmm, Gromas, Amber etc > > to describe different protein systems with all-atoms model. > > > > Sometimes protein is so huge that we have to consider another way to > > deal with it. For example, we introduce new algorithm (Cell multipole > > method, PPPM) to reduce computation time, or we resort to parallel > > program. I am curious that does anyone has develop the general force > > field (epslo, sigma, charge) for only 20 acid amio residues if we > > treat each residue as one atom. If yes, could you please give me a > > reference paper? --------------------------------------------------------------------------- 1. Tommi Hassinen Hassinen T.; Perdkyld M. J Comput Chem 22, 1229-1242 (2001) I have used 1-3 mass points / amino acid residue, and a solvent-accessible surface based solvation model. The program is also available (with source code) at http://www.bioinformatics.org/ghemical ----------------------------------------------------------------------------- 2. Konrad Hinsen A simple harmonic forcefield for a one-particle-per-residue model is described in the following paper: K. Hinsen, A.J. Petrescu, S. Dellerue, M.C. Bellissent-Funel, G.R. Kneller Harmonicity in slow protein dynamics Chem. Phys. 261, 25-37 (2000) The paper also shows that this forcefield plus harmonic Brownian dynamics (Brownian modes) gives excellent results for dynamic quantities (correlation functions) over a large time range. An implementation of this technique is available in the Molecular Modelling Toolkit, to be found at http://dirac.cnrs-orleans.fr/MMTK/ -------------------------------------------------------------------------------- 3. Richard Gillilan "Energy-based de novo protein folding by conformational space annealing and an off-lattice united-residue force field: Application to the 10-55 fragment of staphylococcal protein A and to apo calbindin D9K" P NATL ACAD SCI USA 96 (5): 2025-2030 MAR 2 1999 I also remember a paper by T. Head-Gordon & Brooks in which residues are treated as multipoles: BIOPOLYMERS 31 (1): 77-100 JAN 1991 ----------------------------------------------------------------------------------- 4. Masakatsu Watanabe 1) Troyer et.al. utilize the simple point-per-residue potential developed by Miyazawa & Jernigan to perform the Langevin dynamics. (Check http://www.cmpharm.ucsf.edu/~troyer/eccc/toc.html). 2) The other approaches are to simplify amino acid residues by more than one interaction point; - The Head-Gordon & Brooks approach are described as the Virtual body Dynamics (See Biopolymers, 31, p 77, 1991). In their approach, however, the development of electrostatic potential is not so simple. Therefore, we took their representations of residues and developed our unique potential by defining the pair distribution function, described by Bahar et. al. (See PROTEINS, 29, p292, 1997), from the selected protein molecules. This develop potential was used in the simulation. - Haliloglu and Bahar (See Proteins, 31, p271, 1998) had also utilized their developed a coarse-grain potential for their MD simulations. - The coarser representation of residue is done by Herzyk and Hubbard (See PROTEINS, 17, p310, 1993). They used their residue representations in the content of NMR refinement, but their representation can be utilized to develop unique potential for the dynamics simulation. ------------------------------------------------------------------------------- 5. Dr. David N. Haney C.E. Padilla, H.E. Alper, D.N. Chin, M. Watanabe, V. Karlov, K.B. Blair, H.M. Chun, O. Becker, L. Caves, R. Nagle, M. Karplus, and D.N. Haney (2000) J. Comp. Chem., 21(3): 159-184 "A Substructured Modeling Approach for Long Time Molecular Dynamics Simulations" -------------------------------------------------------------------------------- I really appreciate for your helping. Jie From chemistry-request@server.ccl.net Fri Apr 12 19:06:09 2002 Received: from mo.schrodinger.com ([192.156.98.50]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3CN69j24059 for ; Fri, 12 Apr 2002 19:06:09 -0400 Received: from localhost (jshelley@localhost) by mo.schrodinger.com (SGI-8.9.3/8.9.3) with ESMTP id QAA46533; Fri, 12 Apr 2002 16:05:19 -0700 (PDT) X-Authentication-Warning: mo.schrodinger.com: jshelley owned process doing -bs Date: Fri, 12 Apr 2002 16:05:19 -0700 From: John Shelley To: Patrick Laine cc: chemistry@ccl.net Subject: Re: CCL:Macromodel: error generating interactions In-Reply-To: <003301c1e240$d6373090$3f504a81@vivaldi> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Wayne, Its hard to know for sure what the precise problem is in this case. Would you send this to help@schrodinger.com along with the .com, input structure file (likely the .dat file), the substructure file (if you are using one... usually the .sbc file), and the .log file, please? An we will try to help you out. Have you tried a different forcefield (e.g. OPLS-AA)? Regards, John Shelley Senior Scientist, Schrodinger, Inc. PS. There's an independent user's group mailing list: mmodlist@chem.iupui.edu for MacroModel you might want to join that list too (we participate in that list too). On Fri, 12 Apr 2002, Patrick Laine wrote: > I am trying to submit a conformational search(Monte Carlo) using macromodel and the amber force field and the job will not run because when the program tries to load the parameters from the force field I get a message saying: > INTFFC: No nonbonded params in force field for atom type 17 (OA) > INTFFC: No nonbonded params in force field for atom type 29 (NC) > INTFFC: No nonbonded params in force field for atom type 33 (NE) > INTFFC: No nonbonded params in force field for atom type 34 (NF) > INTFFC: No nonbonded params in force field for atom type 35 (NG) > UPDATE_INT: INTFFC fails > Monitored BatchMin job completed. > Error generating interactions; see LOG file > > When I view the force field and all of the nonbonded params within, I find no problem. I look for those specific atoms listed above, and I can still not find the problem. I have tried to redraw those atoms in macromodel, but that doesn't work either. > > Your help would be greatly appreciated, > Thank you, > > Patrick Laine > Graduate Student > University of Notre Dame > Department of Chemistry and Biochemistry > 372 Stepan Hall > Work: 574-631-4007 > From chemistry-request@server.ccl.net Fri Apr 12 21:13:16 2002 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3D1DGj25358 for ; Fri, 12 Apr 2002 21:13:16 -0400 Received: from arlen.ccl.net (arlen.ccl.net [192.148.249.10]) by ccl.net (8.11.6+Sun/8.11.6/OSC 2.0) with ESMTP id g3D1DG329973; Fri, 12 Apr 2002 21:13:16 -0400 (EDT) Date: Fri, 12 Apr 2002 21:13:15 -0400 (EDT) From: Jan Labanowski To: chemistry@ccl.net cc: Jan Labanowski , anatoli.korkin@motorola.com Subject: 02.09.10 Nano and Giga Challenges in Microelectronics -- Moscow Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Computational Chemistry List, Please, find the latest update on the Nano and Giga Challenges in Microelectronics conference in Moscow. It contains a significant computational materials science component. The CCL (through its coordinator jkl@ccl.net (Jan K Labanowski {:-)}) is also involved in organizing other meetings with important computational materials science and computational chemistry components. Pointers at: http://www.ccl.net CHECK IT OUT!!! All the best... Try to stay calm in these trying times... And for the participants of ACS@Orlando, welcome back home {:-)} (except these guys, who stay a little bit longer and enjoy...). Jan ============================================================================= Symposium and Summer School on Nano and Giga Challenges in Microelectronics Research and Opportunities in Russia Moscow, September 10-13, 2002 http://www.AtomicScaleDesign.Net/Moscow CONFERENCE BACKGROUND ===================== An essential enabler of the information society -- microelectronics -- is a field at the threshold of a new phase. The next stage, involving nanometer scale structures, and integration levels including billions of transistors, presents a number of unprecedented challenges in their practical realization, and requires new materials, new technologies in photolithography and semiconductor processing, new devices, and new design strategies. Russia, with its large intellectual potential, outstanding education system, and strong scientific tradition, is in the position to make a significant contribution toward solving these challenges. This meeting is dedicated to bringing together scientists and engineers from academia, industry and national labs to discuss recent achievements and collaborative efforts in solving these problems. MEETING FORMAT ============== The scientific program includes a Summer School (first 2 days) and a Symposium (last 2 days). The Summer School program consists of tutorial (plenary) lectures followed by panel discussions involving both participants and speakers. The Symposium includes plenary sections in the morning, which are followed by oral presentations and poster sessions in the afternoon. Evening sessions will focus on technology trends and collaborative discussions. TECHNICAL SCOPE =============== Abstracts are invited in the following areas: * atomic scale design: theory and experiment * fabrication of nanodevices * highest frequency electronics * integrated and subwave optoelectronics * magnetic materials and spintronics * molecular electronics * new materials and processes for future FETs * nanotubes: future wires and other devices * non-silicon materials and devices * predicting global technology trends * quantum effects in devices * system design technologies * tutorials on nanotechnology and nanoelectronics CONFERENCE CO-CHAIRMEN ====================== Evgeniy Velikhov (Kurchatov Institute, Russia) and Andreas Wild (DDL Motorola, Germany) ORGANIZING & PROGRAM COMMITTEE ============================== Boris Aronzon, Alexander Bagatur'yants, Gennadi Bersuker, Vladimir Betelin, Dmitry Borisov, Bruno Chaudret, Evgeniya Davidova, Alex Demkov, Rickey Faehl, Stanislav Fedulov, Konstantin Golant, Alexey Golubev, Jim Greer, Evgeniy Gusev, Pavel Kashkarov, Anatoli Korkin (co-chairman), Jan Labanowski, Maria Oseeva, Dmitry Panfilov, Boris Potapkin (co-chairman), Doug Resnick, Irene Rybakova, Elena Shulakova, Alex Volinsky, Alexander Zakharov, Yekaterina Zikeeva SCIENTIFIC & ADVISORY BOARD =========================== Michail Alfimov, Vitaliy Aristov, Boris Borisov, Rick Brzozowy, Evgeniy Dianov, Edward Hall, Takeo Hattori, Siegfried Hecker, Radiy Il'kayev, William Johnson, Carl Kutche, Gerald Lucovsky, Evgeniy Meilikhov (co-chairman), Marius Orlowski (co-chairman), David Pappas, Vladimir Rusanov, Paul Siffert, Jim Toevs SPONSORS ======== Digital DNA Lab Motorola, Russian Research Center Kurchatov Institute, Nuclear Cities Initiative, Nuclear Threat Initiative, Moscow State University, Russian Federal Nuclear Center, European Office of Aerospace Research and Development United States Air Force SPEAKERS ======== Gennadi Bersuker, Alex Bratkovski, Bruno Chaudret, Ramon Compano, Gabriel Crean, Roger Elliott, David Ferry, Julian Gale, David Gilmer, Willam Goddard III, Eugene Golant, Alexander Granovski, David Graves, Vladimir Gritsenko, Detlev Gruetzmacher, Evgeni Gusev, Takeo Hattori, Scott Hector, Howard Huff, Mitsuteru Inoue, Natalia Kirova, Nikolay Kukhtarev, Kaupo Kukli, Patrick Lenahan, Konstantin Likharev, Gerald Lucovsky, Evgeni Meilikhov, Oleg Okhotnikov, Alexander Popov, Efim Portnoi, Victor Printz, Ronald Pyle, Nikolai Rambidi, Mark Schattenburg, Otto Sankey, Konstantin Svidzinskiy, Peter Ventzek, Victor Veselago, Alex Volinsky, Ken-Ichi Ueda Details about the program, registration, abstracts, publication, venue, visas, financial aid, Moscow, etc., etc., available at the web site: http://asdn.net/moscow We are looking forward to see you at our meeting in Moscow!