From chemistry-request@server.ccl.net Fri Jul 26 04:12:14 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 g6Q8CDr06546 for ; Fri, 26 Jul 2002 04:12:13 -0400 Received: from sun14.ccdc.cam.ac.uk ([131.111.113.48] helo=ccdc.cam.ac.uk) by jeeves.ccdc.cam.ac.uk with esmtp (Exim 3.35 #1 (Debian)) id 17Y0Cq-0000fZ-00; Fri, 26 Jul 2002 09:12:12 +0100 Sender: jaccos@ccl.net Message-ID: <3D410457.D9B65A48@ccdc.cam.ac.uk> Date: Fri, 26 Jul 2002 09:12:07 +0100 From: Jacco van de Streek Organization: CCDC X-Mailer: Mozilla 4.7 [en] (X11; I; SunOS 5.8 sun4u) X-Accept-Language: en MIME-Version: 1.0 To: Marcin Krol CC: chemistry@ccl.net Subject: Re: CCL:Merz-Kollman charges - constraints References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Marcin Krol wrote: > > Dear CCL'ers > > I'm using MK charge fitting scheme as impl;emented in Gaussian98 for a > symmteric molecule. However, charges, which should be equivalent, differ > for about 0.1e. Increasing number of points doesn't help. Do you know of > any program which would constrain charges on equivalent atoms before the > fit (like in RESP or CHELP-BOW methods)? Or maybe Gaussian can do it? In my experience with Gaussian94, using the Breneman CHelpG instead of the Merz-Kollman set of sampling points solves the problem (replace pop=MK with pop=CHelpG). I think this has to do not only with the number of points, but also with the way they are chosen. Constraining the atomic charges to reproduce the QM dipole moment will also help: pop=(CHelpG,dipole). Neither of these suggestions mathematically constrains charges on symmetry-equivalent atoms, but I have found that in practice the charges on symmetry-equivalent atoms are usually identical or nearly identical (within, say, 0.01 e). Switching from MK to CHelpG has the added advantage (in Gaussian94) that Gaussian will not crash if you ever need the ReadRadii key word (for elements for which no Van der Waals radii are stored within Gaussian, like bromine). Best wishes, -- Jacco van de Streek Research Scientist Cambridge Crystallographic Data Centre Cambridge United Kingdom From chemistry-request@server.ccl.net Fri Jul 26 04:55:04 2002 Received: from crane2.cf.ac.uk ([131.251.0.25]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6Q8t4r07632 for ; Fri, 26 Jul 2002 04:55:04 -0400 Received: from thor.cf.ac.uk ([131.251.0.1]) by crane2.cf.ac.uk with esmtp (Exim 3.03 #1) id 17Y0sK-0002vr-00 for CHEMISTRY@ccl.net; Fri, 26 Jul 2002 09:55:04 +0100 Received: from localhost (sacjap@localhost) by thor.cf.ac.uk (8.8.8/8.6.12) with ESMTP id JAA10954 for ; Fri, 26 Jul 2002 09:55:03 +0100 (BST) Date: Fri, 26 Jul 2002 09:55:03 +0100 (BST) From: Jamie Platts X-Sender: sacjap@thor To: CHEMISTRY@ccl.net Subject: PES scan in G98 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, When running PES scans in G98 using Opt=ModRedundant, I often get errors such as below: Iteration 99 RMS(Cart)= 0.00000107 RMS(Int)= 0.00536936 Iteration100 RMS(Cart)= 0.00000107 RMS(Int)= 0.00536908 Curvilinear step not converged. Error imposing constraints Error termination via Lnk1e in /home/colossus/jamie/g98/l103.exe. which seems to be just short of convergence. I can't see anything in the manual which might relax this criterion, or allow more iterations, so I'm a bit stuck. Does anyone have any idea how I can fix this? Am I simply using too large a step size (30 degrees in a dihedral in this case)? ---------------------------------------------------------- Jamie Platts Dept. of Chemistry Phone: +44 (0) 2920 874950 Cardiff University Email: platts@cf.ac.uk P.O. Box 912 FAX: +44 (0) 2920 874030 Cardiff CF10 3TB www.cf.ac.uk/chemy From chemistry-request@server.ccl.net Fri Jul 26 11:56:52 2002 Received: from racerx.caregroup.harvard.edu ([134.174.222.35]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6QFuqr16657 for ; Fri, 26 Jul 2002 11:56:52 -0400 Received: from exchange.caregroup.harvard.edu (exchange.caregroup.harvard.edu [134.174.222.55]) by racerx.caregroup.harvard.edu (Switch-2.1.3/Switch-2.1.0) with ESMTP id g6QFun823646 for ; Fri, 26 Jul 2002 11:56:49 -0400 Received: by exchange.caregroup.harvard.edu with Internet Mail Service (5.5.2653.19) id ; Fri, 26 Jul 2002 11:56:52 -0400 Message-ID: From: cchoi@caregroup.harvard.edu To: chemistry@ccl.net Subject: Problem with Autodock 3.0: ATOM_MAPS variable Date: Fri, 26 Jul 2002 11:56:49 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain Hello, this is my first posting. I am having a problem when I run a calculation using acetyl-CoA, because there are 7 atom types used, and the default for Autodock 3.0 is 6. This causes autodock3 to crash, and I get the following (the path has been edited): --------------- /autodock3/bin/autodock3: ERROR: ERROR: 7 atom types declared in "A", S_line "CANOPSH"; maximum allowed is 6. Change "ATOM_MAPS" in "autocomm.h" /autodock3/bin/autodock3: Aborting... /autodock3/bin/autodock3: Unsuccessful Completion. ------------------ When I do change either ATOM_MAPS or MAX_MAPS (or both) in autocomm.h, the compile fails. Any suggestions would be greatly appreciated. I am running Redhat LINUX 7.3 on a dual AMD MP workstation. Sincerely, Chu Choi, Ph.D. cchoi@caregroup.harvard.edu From chemistry-request@server.ccl.net Fri Jul 26 12:29:48 2002 Received: from hermes.csd.unb.ca (root@[131.202.3.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6QGTmr17322 for ; Fri, 26 Jul 2002 12:29:48 -0400 Received: from mailserv2 (mailserv.unb.ca [131.202.3.23]) by hermes.csd.unb.ca (8.12.3/8.12.3) with SMTP id g6QGTigZ027798 for ; Fri, 26 Jul 2002 13:29:44 -0300 (ADT) Received: FROM pop.unb.ca BY mailserv2 ; Fri Jul 26 13:29:43 2002 -0300 Received: from webmail1 (webmail1.unb.ca [131.202.130.26]) by pop.unb.ca (8.9.3/8.9.3) with ESMTP id NAA28345; Fri, 26 Jul 2002 13:29:43 -0300 (ADT) X-WebMail-UserID: l72k6 Date: Fri, 26 Jul 2002 13:29:43 -0300 Sender: Robert Flight From: Robert Flight To: cchoi@caregroup.harvard.edu, Computational Chemistry List X-EXP32-SerialNo: 00003025, 00003442 Subject: RE: CCL:Problem with Autodock 3.0: ATOM_MAPS variable Message-ID: <3D405EB0@webmail1> Mime-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Mailer: WebMail (Hydra) SMTP v3.61.08 Dear Chu, I went through this problem myself. How are you compiling the source code?? Are you using the "make" file included with the source code? What kind of errors are you getting from the compiler? I had no problems compiling on my machine (Pentium 4 running Redhat Linux 7.3). Robert >===== Original Message From cchoi@caregroup.harvard.edu ===== >Hello, this is my first posting. > >I am having a problem when I run a calculation using acetyl-CoA, because >there are 7 atom types used, and the default for Autodock 3.0 is 6. This >causes autodock3 to crash, and I get the following (the path has been >edited): > >--------------- >/autodock3/bin/autodock3: ERROR: ERROR: 7 atom types declared in "A", S_line >"CANOPSH"; maximum allowed is 6. >Change "ATOM_MAPS" in "autocomm.h" >/autodock3/bin/autodock3: Aborting... > >/autodock3/bin/autodock3: Unsuccessful Completion. >------------------ > > >When I do change either ATOM_MAPS or MAX_MAPS (or both) in autocomm.h, the >compile fails. Any suggestions would be greatly appreciated. > >I am running Redhat LINUX 7.3 on a dual AMD MP workstation. > >Sincerely, >Chu Choi, Ph.D. >cchoi@caregroup.harvard.edu > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net ******************************** Robert Flight Masters Student Department of Chemistry University of New Brunswick Fredericton, NB Canada E3B 6E2 e-mail: L72K6@unb.ca ******************************** From chemistry-request@server.ccl.net Fri Jul 26 08:00:32 2002 Received: from hotmail.com ([64.4.19.139]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6QC0Vr11494 for ; Fri, 26 Jul 2002 08:00:31 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Fri, 26 Jul 2002 05:00:27 -0700 Received: from 129.173.17.185 by lw12fd.law12.hotmail.msn.com with HTTP; Fri, 26 Jul 2002 12:00:26 GMT X-Originating-IP: [129.173.17.185] From: "Jackie Wu" To: chemistry@ccl.net Subject: Trajectory calculation Date: Fri, 26 Jul 2002 08:00:26 -0400 Mime-Version: 1.0 Content-Type: text/html Message-ID: X-OriginalArrivalTime: 26 Jul 2002 12:00:27.0300 (UTC) FILETIME=[07F78640:01C2349C]
Dear cclers,
 
I am trying to do a direct dynamics trajectory calculation on a test example. But it seems there is a syntax error in my input file. I have checked the Gaussian manual, but did not find a clue. Does anybody knows what is going on? The input keywords are :
 
# b3lyp/6-31g(d) traj(ntraj=20, steps=100, phase(1,3), rtemp=500) geom=crowd
 
 QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT LINE.
 G(D) GEOM=CROWD # TRAJ(NTRAJ=20,STEPS=10
                                                      '
 Last state="Trj2"
 TCursr=10128 LCursr=  35
 Error termination via Lnk1e in /home/jgauld/g98/l1.exe.
 
It seems that the keywords in the bracket following Traj does not correct.
 
Thanks.
 
Zhijian WU

MSN Photos is the easiest way to share and print your photos: Click Here
From chemistry-request@server.ccl.net Thu Jul 25 13:28:46 2002 Received: from mxout3.cac.washington.edu ([140.142.32.19]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6PHSkr06606 for ; Thu, 25 Jul 2002 13:28:46 -0400 Received: from mailscan-out1.cac.washington.edu (mailscan-out1.cac.washington.edu [140.142.32.17]) by mxout3.cac.washington.edu (8.12.1+UW01.12/8.12.1+UW02.06) with SMTP id g6PHSfYu031275 for ; Thu, 25 Jul 2002 10:28:41 -0700 Received: FROM hymn07.u.washington.edu BY mailscan-out1.cac.washington.edu ; Thu Jul 25 10:28:40 2002 -0700 Received: from localhost (localhost [127.0.0.1]) by hymn07.u.washington.edu (8.12.1+UW01.12/8.12.1+UW02.01) with ESMTP id g6PHSejn029573 for ; Thu, 25 Jul 2002 10:28:40 -0700 Date: Thu, 25 Jul 2002 10:28:40 -0700 (PDT) From: Christophe L M J Verlinde To: chemistry@ccl.net Subject: free energy calc In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; CHARSET=US-ASCII Dear CCLers, We have been trying to "predict" the free energy change for replacing a neutral inhibitor bound to a protein into an isosteric one with a -1 charge via a thermodynamic cycle. Our approach consists of MD simulations with and explicit waters (TIP3P). We have tried both FEP and TI. We also experimented with particle mesh Ewald techniques. The bottom line is that the calculations are off by 2.5 to 5 kcal/mol > from reality depending on the protocol (we used the AMBER6 package). The problem probably does not reside in proper sampling as the simulations reproduce the conformational change seen between the 2 complexes (we have high resolution X-ray structures). Has anyone had any success with such type of simulations, i.e. cases involving a net change in charge? If so, could you provide us with recommended protocols. Thanks Christophe L.M.J. Verlinde Biomolecular Structure Center University of Washington - Box 357742 Seattle, WA 98195 T:(206)543-8865 F:(206)685-7002 URL: www.bmsc.washington.edu/people/verlinde From chemistry-request@server.ccl.net Thu Jul 25 18:17:11 2002 Received: from trickle.cc.mcgill.ca ([132.206.27.51]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6PMHBr16095 for ; Thu, 25 Jul 2002 18:17:11 -0400 Received: from rna.mcgill.ca (rna.McGill.CA [132.206.27.47]) by trickle.cc.mcgill.ca (8.12.3/8.11.0) with ESMTP id g6PMHArw018752 for ; Thu, 25 Jul 2002 18:17:10 -0400 (EDT) Received: from mcgill (ariya3.Chem.McGill.CA [132.206.175.121]) by rna.mcgill.ca (8.12.2/8.12.0) with ESMTP id g6PMH96Z021947 for ; Thu, 25 Jul 2002 18:17:09 -0400 (EDT) From: "Alexei Khalizov" To: chemistry@ccl.net Date: Thu, 25 Jul 2002 18:17:09 -0400 MIME-Version: 1.0 Subject: SUMMARY: A problem with O(1D) Reply-to: alexei.khalizov@mcgill.ca Message-ID: <3D4040A4.30111.18E9CFB@localhost> Priority: normal X-mailer: Pegasus Mail for Windows (v4.01) Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT Content-description: Mail message body This is a SUMMARY of the answers on my question about the calculation of the correct energy of singlet oxygen atom O(1D). I am very grateful for all responses I received, which helped to shed some light upon the problem. In short words, the 1D state cannot be represented with a single determinant so there is no an easy way to get around it using DFT theory. MCSCF can solve the problem. Using MP2 with complex orbitals might be prominent as well. Composite model chemistry G3 or coupled clusters including triple and maybe quadruple excitations with sufficiently extended basis set may be of help. Since convergence of the inter-pair correlation energy with the size of basis set is slow, using a basis set extrapolation formula might be necessary in the latter case. Besides, most basis sets are optimised and contracted for the ground states of atoms, which leads to overestimation of their excitation energies. By now, I have tried G3 and CCSD(T)/aug-cc- pVQZ, which resulted in 8.5 and 20.5 kJ/mol overestimation of the experimental value, respectively. In the latter case T1 value is small, 0.004. Regards, Alexei ---------------------- Dear CCLers, Does anyone know how to calculate correctly the energy of an oxygen atom in the singlet state O(1D)? I am having a problem of evaluating the singlet-triplet energy difference E(S-T) = E[O(1D)] - E[O(3P)] whose experimental value is 190 kJ/mol. Using DFT methods (B3LYP and PW91) with small basis sets (6-31G*) significantly overestimates this energy splitting, giving E(S-T) = 270-280 kJ/mol. Calculation at CCSD(T)/6-311+G(3df) level of theory leads to a better result, however, it is still far from being acceptable, E(S-T) = 214 kJ/mol. So far I have found that it is the energy of O(1D) that is incorrect while the energy of O(3P) is reproduced properly. What goes wrong? The wavefunction for O(1D) seems to be correct - population analysis shows that it is symmetrical (2Px alpha) (2Px beta) (2Py alpha) (2Py beta). Thank you in advance, Alexei ---------------------- Dear Alexei, You can try correlation consistent basis set, e.g. aug-cc-pVTZ, which is better suited for electron correlation calculations than the conventional Pople basis. Best regards, Victor. Victor Anisimov, Krakow, Poland. ---------------------- Hi Alexei, I am not sure what the problem is but I'll give you my view anyway. First of all your problem reminds me of the singlet-triplet splitting of methylene. This is a well know benchmark problem for post Hartree- Fock treatments. One not only needs to recover a large fraction of the correlation energy to get it right but the basis set requirements for the 2 states are quite different as well. So as far as your CCSD(T) results are concerned the basis set might be the problem. Second using DFT I don't think your 1D state can be represented as a single Slater determinant. In that case you can still do DFT but you need special energy expressions (see e.g. the work of Filatov and Shaik, CPL 304 (1999) 429-437). Are you sure that your code supports such expressions? Best wishes, Huub Huub van Dam E-mail: h.j.j.vandam@dl.ac.uk CCLRC Daresbury Laboratory phone: +44-1925-603362 Daresbury, Warrington fax: +44-1925-603634 Cheshire, UK WA4 4AD ---------------------- Getting the 1D state for O requires a two-determinant wave function, or alternatively using complex orbitals for a single determinant. A single determinant RHF type wave function is a mixture of the 1D and 1S states, which is why you are getting a too high value. You can model the 1D with a small MCSCF (many programs) or using complex orbitals (Gaussian is the only one I know of). With the latter, you can include correlation with MP2, but I don't know any other methods/programs availabel. MP2, however, gives a fairly decent description of the singlet-triplet energy difference, but you are presumably after something more than just this value(?). Frank | Frank Jensen, Department of Chemistry | | University of Southern Denmark | | Campusvej 55, DK-5230 Odense, Denmark | | FAX +45 66 15 87 80 , Voice +45 65 50 25 07 | | http://www.sdu.dk/Nat/Chem/STAFF/sci/FrjE.html | | http://bogense.chem.ou.dk/~frj ---------------------- The S/T splitting is very hard to calculate, because the intrapair correlation energy converges very slow with the basis set size. Two states of oxygen have different number of electron pairs (or beta electrons, assuming each beta electron is paired with an alpha one). If you apply an empirical correction to account for this, as it is done in G3 theory [JCP, 109, 7764 (1998); I'm talking about the HLC correction, Eq. 6], your difference will drop by another 10 kJ/mol. Since the basis set used in G3 theory is slightly different (it includes core correlation functions, which your set is missing), the agreement between theory and experiment becomes OK. To summarize: nothing seems wrong with your calculations. The computational models you are using can go only that far. Vitaly Rassolov Dept. of Chemistry and Biochemistry (803) 777-7811 University of South Carolina fax (803) 777-9521 631 Sumter St Columbia, SC 29208 rassolov@mail.chem.sc.edu ---------------------- Hi Alexei, as always, it might be either a correlation problem or a basis set problem. Within CC theory, the size of the largest T1 and T2 amplitudes is a qualitative measure of the importance of correlation. When both are smaller than maybe 0.05 CCSD(T) usually gives very accurate energy differences. When one of them (especially the largest T2-amplitude) is larger than ~0.10, the quality may suffer visibly. In the latter case inclusion of higher excitations is helpful, e.g. CCSD(TQ). The size of the largest T1-amplitude may depend on the choice of reference function (UHF, ROHF, QRHF, ...). The other part is basis sets, quite possibly more important here. Most basis sets are optimized and contracted for the ground states of atoms (3P for O). Therefor the excitation energies from the ground state to excited states are prone to be too large, especially for small basis sets. The way out is to use basis set extrapolation. It has been shown to be reliable for many properties with the cc-basis sets of Dunning and co-workers. A good formula is found in Peterson, Woon, Dunning, J. Chem. Phys. 100, 7410 ('94), equation 2. Stefan Dr. Stefan Fau fau@qtp.ufl.edu University of Florida (352) 392-6714 Quantum Theory Project 2319 NPB #92, P.O.Box 118435 Gainesville, FL 32611-8435 ------------------------- Dr. Alexei Khalizov Department of Chemistry McGill University, 801 Sherbrooke St. W., Montreal, Quebec, CANADA, H3A 2K6 Phone: (514) 398-6920 Fax: (514) 398-2382 From chemistry-request@server.ccl.net Fri Jul 26 12:47:33 2002 Received: from hotmail.com ([64.4.15.198]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6QGlXr18002 for ; Fri, 26 Jul 2002 12:47:33 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Fri, 26 Jul 2002 09:47:28 -0700 Received: from 128.235.242.51 by lw10fd.law10.hotmail.msn.com with HTTP; Fri, 26 Jul 2002 16:47:28 GMT X-Originating-IP: [128.235.242.51] From: "Deepangi Pandit" To: cchoi@caregroup.harvard.edu, chemistry@ccl.net Subject: Re: CCL:Problem with Autodock 3.0: ATOM_MAPS variable Date: Fri, 26 Jul 2002 12:47:28 -0400 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 26 Jul 2002 16:47:28.0476 (UTC) FILETIME=[209671C0:01C234C4] Hello: Just few days back on Wed, 17 Jul 2002 Robert Flight has compiled summary of this question .Please visit follwing link: http://www.ccl.net/cgi-bin/ccl/message.cgi?2002+07+17+003 I feel it will solve your problem. Deepangi From: cchoi@caregroup.harvard.edu To: chemistry@ccl.net Subject: CCL:Problem with Autodock 3.0: ATOM_MAPS variable Date: Fri, 26 Jul 2002 11:56:49 -0400 Hello, this is my first posting. I am having a problem when I run a calculation using acetyl-CoA, because there are 7 atom types used, and the default for Autodock 3.0 is 6. This causes autodock3 to crash, and I get the following (the path has been edited): --------------- /autodock3/bin/autodock3: ERROR: ERROR: 7 atom types declared in "A", S_line "CANOPSH"; maximum allowed is 6. Change "ATOM_MAPS" in "autocomm.h" /autodock3/bin/autodock3: Aborting... /autodock3/bin/autodock3: Unsuccessful Completion. ------------------ When I do change either ATOM_MAPS or MAX_MAPS (or both) in autocomm.h, the compile fails. Any suggestions would be greatly appreciated. I am running Redhat LINUX 7.3 on a dual AMD MP workstation. Sincerely, Chu Choi, Ph.D. cchoi@caregroup.harvard.edu -= This is automatically added to each message by mailing script =- CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net Deepangi _________________________________________________________________ MSN Photos is the easiest way to share and print your photos: http://photos.msn.com/support/worldwide.aspx From chemistry-request@server.ccl.net Thu Jul 25 18:24:38 2002 Received: from mx.seanet.com ([199.181.164.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6PMObr16311 for ; Thu, 25 Jul 2002 18:24:37 -0400 Received: from Debug (ssl.seanet.com [199.181.164.13]) by mx.seanet.com (8.11.6/8.11.6) with SMTP id g6PMONR04598; Thu, 25 Jul 2002 15:24:23 -0700 (PDT) Message-Id: <200207252224.g6PMONR04598@mx.seanet.com> To: Andrew Ryzhkov , CCL From: Mark Thompson Subject: Re: CCL:Programs for drawing the molecular structure for papers Date: Thu, 25 Jul 2002 15:24:31 US/Pacific X-Mailer: Endymion MailMan Professional Edition v3.0.35 If you want 2D pictures like you see in Organic Chem texts, programs like Chem3D will probably do what you want. If you want a high quality 3D image with bond lengths, angles, etc printed along with the molecular structure, then most of the commercial modeling packages should do what you want. For example, ArgusLab will export high quality molecular images with geometry monitors to bitmap, JPEG, and TIFF files (which can then be imported into MS Word, etc.). Also, you can export to POV-Ray files which can be rendered by the free ray-tracing utility POV-Ray (www.povray.org) to very high quality images. ArgusLab can be obtained at http://www.arguslab.com Cheers, Mark > Dear CCL'ers > > What programs do you use for representing geometry parameters of > the molecules in papers? > A program of this kind have to plot a molecular structure > in black&white (not gray) as ball&sticks and > if it's possible to print bond lengths and angles. > > > > Thank you and best regards, > Andrew > > > > > Dr. Andrei Ryjkov > Departments of Chemistry, and Atmospheric and Oceanic Sciences, > McGill University, > 805 Sherbrooke St. West #808 > Montreal, Quebec, CANADA, > H3A 2K6. > ---------------------------------------------------------------- > E-mail: Andrew@Zephyr.Meteo.McGill.Ca > Internet: http://RedAndr.tripod.com > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > ======================================= Mark Thompson, Ph.D. Planaria Software Seattle, WA http://www.arguslab.com ======================================= From chemistry-request@server.ccl.net Fri Jul 26 15:40:17 2002 Received: from speedracer.caregroup.harvard.edu (IDENT:root@[134.174.222.36]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6QJeGr22234 for ; Fri, 26 Jul 2002 15:40:17 -0400 Received: from exchange.caregroup.harvard.edu (exchange.caregroup.harvard.edu [134.174.222.55]) by speedracer.caregroup.harvard.edu (Switch-2.1.3/Switch-2.1.0) with ESMTP id g6QJeHQ14226 for ; Fri, 26 Jul 2002 15:40:17 -0400 Received: by exchange.caregroup.harvard.edu with Internet Mail Service (5.5.2653.19) id ; Fri, 26 Jul 2002 15:40:17 -0400 Message-ID: From: cchoi@caregroup.harvard.edu To: chemistry@ccl.net Subject: Compilation problem - Autodock 3.0 - ATOM_MAPS variable in autoco mm.h Date: Fri, 26 Jul 2002 15:40:16 -0400 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain Hello CCLers, I have a perplexing problem, and I'd like to give more details about what I posted before. 1) The autodock3 binary only handles 6 atom types by default. I was able to compile this okay. 2) When I try to call the program using acetyl-CoA as a ligand, it crashes, telling me to recompile, changing the ATOM_MAPS variable in autocomm.h. 3) When I change this variable, it fails to compile and gives error messages of the type: [donald@localhost autodock]$ make gcc -DNDEBUG -O3 -c -DWRITEPDBQSTATE main.cc gcc -DNDEBUG -O3 -c call_gs.cc gcc -DNDEBUG -O3 -c -DEINTCALPRINT cmdmode.cc gcc -DNDEBUG -O3 -c readmap.cc gcc -DNDEBUG -O3 -c readPDBQ.cc gcc -DNDEBUG -O3 -c eval.cc gcc -DNDEBUG -O3 -c getrms.cc gcc -DNDEBUG -O3 -c getInitialState.cc gcc -DNDEBUG -O3 -c initautodock.cc gcc -DNDEBUG -O3 -c openfile.cc gcc -DNDEBUG -O3 -c -DWRITEMOLASPDBQFUNC writePDBQ.cc -o writeMolAsPDBQ.o gcc -DNDEBUG -O3 -c writePDBQ.cc -o writePDBQ.o gcc -DNDEBUG -O3 -c -DWRITEPDBQSTATE writePDBQ.cc -o writePDBQState.o gcc -DNDEBUG -O3 -c prTorConList.cc gcc -DNDEBUG -O3 -c simanneal.cc gcc -DNDEBUG -O3 -c success.cc gcc -DNDEBUG -O3 -c summarizegrids.cc ar r libad.a call_gs.o cmdmode.o readmap.o readPDBQ.o eval.o getrms.o getInitialState.o initautodock.o openfile.o writeMolAsPDBQ.o writePDBQ.o writePDBQState.o prTorConList.o simanneal.o success.o summarizegrids.o ranlib libad.a echo /usr/local/autodock3/bin ' on '`date`', using '`hostname` >> LATEST_MAKE echo 'Flags: 'gcc -DNDEBUG -O3 -DNOSQRT -L. -lad -lm >> LATEST_MAKE gcc -DNDEBUG -O3 -DNOSQRT -o autodock3 main.o -L. -lad -lm main.o: In function `main': main.o(.text+0x1921): undefined reference to `intnbtable__FPcPiT1iT0ffiiPA13_A13_f' main.o(.text+0x303f): undefined reference to `nbe(char *, _A1 (*)[1], _fi)' main.o(.text+0x538d): undefined reference to `analysis__FiPA127_cPfcT2fPA2_fPA13_A13_ffPA127_A127_A15_fT2ifffiPA1_iiiP5st atePcT2cPA2047_iPiT6T20_fcicT2T2' main.o(.text+0x55a9): undefined reference to `investigate__FiPfcT1PA2_fT4PA13_A13_fffffifffPA127_A127_A15_fiPA1_iiiPA2047 _iPiT4cPA255_UsPccPUsPA7_A1_fT21_cT25_iiff' ./libad.a(cmdmode.o): In function `cmdmode__FilG3tmsfffffffPA127_A127_A15_fPA13_A13_ffPA2_fPA2047_iiiPA1_iPA12 7_cT13_PcPiPfcT22_T20_fi': . . . getInitialState.o(.text+0x4fd): undefined reference to `eintcal(int (*)[1], _A1 (*)[1], _fP, float [2], int *, int, char, float *)' collect2: ld returned 1 exit status make: *** [autodock3] Error 1 4) I have been in touch with Robert Flight and tried his workaround using "autocomm.h-extra-maps". It is sucessful in compiling a new version of autogrid, but autodock3 still fails as above. Changing the variable by hand also causes the compile to fail. 5) If I change autocomm.h back to its default state, autodock3 compiles perfectly. Does anyone know what is happening here? Is there some sort of file or variable interdependency that I am missing? Thank you for any light you may shed on my situation. Sincerely, Donald Choi, Ph.D. Harvard Medical School cchoi@caregroup.harvard.edu From chemistry-request@server.ccl.net Fri Jul 26 14:55:00 2002 Received: from coyote.iupui.edu ([134.68.220.82]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6QIt0r20992 for ; Fri, 26 Jul 2002 14:55:00 -0400 Received: from macgw.chem.iupui.edu (macgw.chem.iupui.edu [134.68.137.71]) by coyote.iupui.edu (8.9.3/8.9.3/IUPUIPO.20020221) with SMTP id NAA30508 for ; Fri, 26 Jul 2002 13:55:01 -0500 (EST) Message-ID: Date: 26 Jul 2002 14:07:27 -0500 From: "Boyd" Subject: Emerging Technologies To: "OSC CCL" X-Mailer: Mail*Link SMTP for Quarterdeck Mail; Version 4.1.0 Hello, What are the latest breakthroughs in computational chemistry? You are invited to hear the talks at the Symposium on Emerging Technologies in Computational Chemistry, to be held at the ACS National Meeting next month. The symposium will be held on Tuesday afternoon, August 20, 2002, in Room 103 of the Hynes Convention Center, Boston, Mass. The speakers will be competing for a $1000 prize sponsored by Schrodinger Inc., www.schrodinger.com The six topics and speakers are: 1. Geminals-based model chemistry. Vitaly A Rassolov (University of South Carolina) 2. A linear-scaling quantum chemistry method for ground and excited states: Localized-density-matrix method. GaunHua Chen (Hong Kong) 3. Monte Carlo simulation of proteins through a random walk in energy space. Nitin Rathore and J. J. de Pablo (University of Wisconsin-Madison) 4. Direct calculation of molecular free energies. Chia-en Chang and M. K. Gilson (University of Maryland) 5. High throughput prediction of passive ADME properties from fragments. Tudor I. Oprea (AstraZeneca and the University of New Mexico), M. Baroni, I. Zamora, and G. Cruciani 6. Priviledged substructure searching for focused set design. Christophe Cleva (Serono Pharmaceutical Research Institute, Switzerland), D. Domine, C. Merlot, J. Bunn, E. Sebille, W. Sauer, and D. Church Hope to see you in Boston. Thanks, Don Donald B. Boyd, Ph.D. Organizer, ACS Annual Symposium on Emerging Computational Technologies Department of Chemistry Indiana University-Purdue University at Indianapolis Indianapolis, Indiana 46202-3274, U.S.A. E-mail boyd@chem.iupui.edu