From aiba@volta.vmsmail.ethz.ch Tue Jul 5 09:46:53 1994 Received: from bernina.ethz.ch for aiba@volta.vmsmail.ethz.ch by www.ccl.net (8.6.9/930601.1506) id JAA12006; Tue, 5 Jul 1994 09:34:29 -0400 Message-Id: <199407051334.JAA12006@www.ccl.net> Received: from VOLTA.vmsmail.ethz.ch by bernina.ethz.ch id <27505-0@bernina.ethz.ch>; Tue, 5 Jul 1994 15:35:17 +0200 X-Vms-To: ethz::"chemistry@ccl.net" To: chemistry@ccl.net From: aiba@volta.vmsmail.ethz.ch (Aiaz Bakassov, Phys. Chem., ETH Zurich) Subject: G92. Core energies. Summary. Date: Tue, 5 Jul 1994 15:35:17 +0200 Dear netters, Some time ago, I posted a question about "how to extract from G92 the core energies H_nn, and, perhaps, the Coulomb integrals J_nm and exchange integrals K_nm?" The only answer came from: ALBERTO GOBBI, gobbi@sg1501.chemie.uni-marburg.de, Bantzerstr. 9, 137.248.151.1, D-35039 Marburg, Tel. 8.00-18.00: 0049 6421 287001, Fax: 0049 6421 285547. Many many thanks to him ! I first summarize about core energies H_nm (which is successful) and then about J_nm and K_nm which was not successful. IMPORTANT: I am reporting ONLY what I tried myself. No one else but me is responsible for my failure with 2-e integrals. The Gaussian92 Programmer's Guide is abbreviated here as G92PG. 0) General advices. ^^^^^^^^^^^^^^^^^^^ --This sort of job requires some extent of Non-Standard Routes and Options. Look at section 4.4 of G92PG starting from page 63. --It is worth to look at *.log file of your job to see what links were executed. Then it is VERY useful to read in the source codes of those links the IOp() parameters meaning and the meaning of the links themselves - you'll learn a lot. 1) Core energies H_nm. ^^^^^^^^^^^^^^^^^^^^^^ To get them from G92 to your *.log file put the following option into the input: IOp(3/33=1) along with your other input. This causes the matrices of kinetic energy, potential energy and of core energies to be printed. These 3 matrices come together always. One can get rid of multipoles matrices and Fermi contact interaction matrices (which also appear together with those 3 matrices) adding to the above option the following one: IOp(3/36=-1) For description of these options look at page 568 of G92PG. 2) Coulomb integrals J_nm ^^^^^^^^^^^^^^^^^^^^^^^^^^ and exchange integrals K_nm. ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ This was not successful. After many trials I cannot get them yet. The idea was to put into the input extralinks=l316 This option is supposed to give 2-e integrals because this link is exactly for "dumping 2-e integrals" as it follows from comments to its source FORTRAN code. For description of extralinks look at page 64 of G92PG. After putting this extralink, I got many-many numbers which I failed to exactly identify (may be someone can do this for us?!). And then error message appeared and G92 terminated abnormally. What did NOT help to improve the situation (including various combinations of options below): -- IOp(3/33=4) -- IOp(3/33=5) -- IOp(3/33=6), [look at page 568 of G92PG for meaning of these IOp's] -- NoSymm [in *.log file this only changed some wording] -- NoRaff [the same as about NoSymm] -- IOp(3/34=2) -- IOp(3/34=3) [page 568 of G92PG] -- extralinks=(311,316) [look at the source codes of those links] That's all I can report about what I myself tried along the advice given to me. So, the core energies are okay and 2-e integrals are NOT. Would very much appreciate further development of this discussion and hints where I've made errors. Very interesting advice came >from help@gaussian.com: "Since I don't know how big your problems are I suggested l804 which has the integrals you requested produced without disk storage and you can start by modifying the output routines to identify the ones you need and discard the rest. Doug Fox." I copied the L804 source code and looked at it. Considering my time schedule, it does not seem feasible for me to revise this code in the nearest future. May be someone else could do it quicker and more professionally. Sincerely, -------------------------------------------------------- -------------- Aiaz BAKASSOV (English: Ayaz BAKASOV) | Phone: +41 1 632 79 18 Laboratorium fuer Phys. Chemie | FAX: +41 1 632 10 21 ETH-Zuerich (Zentrum) | E-mail: aiba@debye.vmsmail.ethz.ch CH-8092 Zurich, Switzerland | aiba@ir.lpc.ethz.ch -------------------------------------------------------- -------------- From cletner@remcure.bmb.wright.edu Tue Jul 5 13:50:39 1994 Received: from remcure.bmb.wright.edu for cletner@remcure.bmb.wright.edu by www.ccl.net (8.6.9/930601.1506) id NAA15543; Tue, 5 Jul 1994 13:08:01 -0400 Received: by remcure.bmb.wright.edu (920330.SGI/921111.SGI.AUTO) for CHEMISTRY@ccl.net id AA13857; Tue, 5 Jul 94 12:58:24 -0700 Date: Tue, 5 Jul 1994 12:45:41 -0700 (PDT) From: Charles Letner Subject: Protonation states in proteins To: Computational Chemistry List Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello all, I am using AMBER to run some MM and MD on proteins. A question that I have begun to ponder is the effect of the protonation state of the acid and basic amino acids on the results. I've been going back over the papers I have on the application of MM & MD to proteins. What I'm finding is that most people really don't say much about which AA's are protonated and which are not. To a first approximation I would expect surface AA's to be charged and interior AA's to be uncharged, though active site residues and salt bridges could obviously be exceptions to this rule. So I'm wonder what those of you in the virtual world think about this? Is it worth going through the trouble to try and determine protonation of each residue? Are there any efficient means of doing this? References and comments of any sort are welcome. I'll send a summary of responses. Thanks Chuck Charles Letner Wright State University Department of Biochemistry Dayton, OH 45435 e-mail: cletner@remcure.bmb.wright.edu From moret@far.ruu.nl Tue Jul 5 17:50:39 1994 Received: from accucx.cc.ruu.nl for moret@far.ruu.nl by www.ccl.net (8.6.9/930601.1506) id RAA19658; Tue, 5 Jul 1994 17:35:33 -0400 Received: from far.ruu.nl (ruucmc.far.ruu.nl) by accucx.cc.ruu.nl with SMTP id AA25807 (5.65c/IDA-1.4.4 for ); Tue, 5 Jul 1994 23:36:33 +0200 Message-Id: <199407052136.AA25807@accucx.cc.ruu.nl> Received: by ruucmc.far.ruu.nl (16.6/16.2) id AA07178; Tue, 5 Jul 94 23:34:35 +0200 From: "E.E.Moret" Subject: Summary: S-charges To: chemistry@ruucmc.far.ruu.nl Date: Tue, 5 Jul 94 23:34:34 METDST Name: Ed Moret Organisation: Utrecht University Phone: 030 - 536979 Mailer: Elm [revision: 66.25] Dear colleagues, Thanks to all who responded so helpfully to my question on sensible S-charges. Some replies indicated even higher S-charges, than the ones I calculated semi-empirically. These results were obtained on quite different compounds, however. Some colleagues computed the charges on my model compound with 6-31++G** and also DFT methods. I intend to use these charges, that are close to +1 for the S-atom. For the bioactive molecules we are studying, I will change the semi-empirical charges only on the sulfonamide-moiety accordingly and leave the rest of the molecules (peptides) as computed. A colleague in Leiden is currently working on the ab initio stuff. Like with Mopac-ESP, CHELPG gives charges comparable to Mulliken with 6-31G* basis sets, according to the calculations from Dr. Guadagnini. As his reply shows, however, the CHELPG 6-31++G** S-charge is only +0.5 !! Some references on the derivation of S-charge for force-fields are highly appreciated. Thanks again. The original messages and the replies are appended. I did not include a Dutch reply, offering me a recent CSD-search which would enable me to check the geometry statistics. With best regards, Ed Moret ************************** From: "E.E.Moret" Subject: CCL:Semi-empirical S-charge: 'right' or 'wrong' ? Date: Sun, 26 Jun 94 13:41:40 METDST Dear colleagues, A good scientific discussion is appropriate and let me be the first to say that I am aware of the fact that my subject line is questionable. There is no right or wrong charge. Atomic point charges are merely a useful concept in computational chemistry. However, the semi-empirical charges I have obtained for the hypervalent S atom are a problem. They disrupt molecular mechanics calculations that I want to perform. I face the problem of accepting these charges or considering them useless for my purpose (docking). Here is my dilemma: We are currently studying molecules with around 100 atoms of which a sulfonamide group is of relevance. Apart from a geometry that does not correpond to X-ray and ab initio information, we observe large positive charges on the S atoms. Some calculation results on the molecule CH3-SO2-NH-CH3 follow. The C-S-N-C torsion angle in the input file was close to the ab initio and X-ray data of 70 or -70. I used MINDO3,MNDO,AM1,PM3 Hamiltonians in Ampac 2.1, Mopac 5, Mopac 6 and Mopac 93. The partial charge on the S atom varied between 1.6 and 2.6 ! Fortunately, there was no programme dependency, apart from programmes that explicitly mentioned the use of a different Hamiltonian for one element. This would be a typical result for the S-charge (Mopac93): sulfa_opt_MINDO3: 6 S 1.849085 sulfa_opt_MNDO: 6 S 1.632472 sulfa_opt_AM1: 6 S 2.526724 sulfa_opt_PM3: 6 S 2.159568 The input-file with cartesian coordinates is appended at the bottom. Besides interesting geometry and charge, the bond orders for the bonds from S to C or N are typically 0.7, whereas the bond orders for the bonds >from S to O are 1.15. I consider the system size prohibitive for ab initio calculations and I hesitate to use an empirical charge calculation. I would value your input on the following questions: - am I wrong in considering the current results conspicuous? - should I accept the current charges, geometry and bond orders? - should I turn to more rigorous or more empirical methods? - should I fiddle the current charges (i.e. changing the S valency by hand and substracting some pos. charge of S and some neg. charge of its neighbouring atoms, which would be a manual reduction? - are their experimental data which would allow me to check whether the current results predict the right interaction or behaviour of S-containing compounds. - will the P atom give comparable results? For those who noticed that I avoided naming P and S. Is it a phosphorus atom and a sulphurous atom or is sulphur and phospor correct english? I am looking forward to your ideas on this topic. AM1 T=3600 NOINTER PRECISE BONDS ./sulfa_opt_AM1.dat 0001 0.0000 0000 0.0000 0000 0.0000 0000 0000 0000 0000 0001 1.7964 0000 0.0000 0000 0.0000 0000 0000 0000 0000 0001 1.4572 0000 3.3222 0000 0.0000 0000 0000 0000 0000 0001 3.5945 0000 3.7754 0000 0.5259 0000 0000 0000 0000 0006 0.8982 0000 0.1420 0000 0.6190 0000 0000 0000 0000 0016 0.8981 0000 1.7989 0000 1.3224 0000 0000 0000 0000 0007 1.6790 0000 3.0433 0000 1.0195 0000 0000 0000 0000 0006 3.1526 0000 2.9846 0000 1.1500 0000 0000 0000 0000 0001 0.8982 0000 -0.5819 0000 1.4472 0000 0000 0000 0000 0001 3.5287 0000 2.0089 0000 0.8086 0000 0000 0000 0000 0001 3.4511 0000 3.1472 0000 2.1961 0000 0000 0000 0000 0008 0.4152 0000 1.4318 0000 2.6394 0000 0000 0000 0000 0008 -0.3714 0000 2.2528 0000 0.7887 0000 0000 0000 0000 From: "E.E.Moret" Subject: CCL:Semi-empirical S-charges II Date: Mon, 27 Jun 94 13:35:16 METDST Dear colleagues, With regards to the question about 'sensible' charges on sulfur atoms: The first responses to my question have arrived (thanks) and suggest to me that I need to clarify 2 things: - the CH3-SO2-NH-CH3 is only a test model for the sulfonamide containing bioactive compounds with approximately 100 atoms. Large basis set ab initio calculations could only be applied to part of the molecules. - Potential derived charges may be the best for modelling purposes and they may be less basis set dependent. Is this correct, even if the basis set lacks incorporation of d-orbitals? I calculated the ESP (Bessler, Merz, Kollman) charges with Mopac93: Molecule Ch3-SO2-nh-ch3 (important atoms in capital letters): Atom Mulliken ESP C -0.82 -0.99 S 2.53 2.45 N -0.78 -0.96 O -0.84 -0.78 O -0.91 -0.88 ************************** Date: Sun, 26 Jun 94 13:36:22 -0400 From: boehm@mulliken.cem.msu.edu (Randy Boehm) Subject: charges_reply The best (arguably) way to get partial atomic charges is to do a fit to the electrostatic potential. I have done such calculations and have found that S in SO4 is about +3. I your MM applications can not handle such values, then get a differenct or develop your own. ************************** Date: Sun, 26 Jun 94 13:02:45 -0700 From: marvin@biosym.com (Marvin Waldman) Subject: Sulfur charges It is indeed an interesting question as to what is the appropriate charge for a hypervalent sulfur attached to so many electronegative atoms (2 oxygens and a nitrogen). My two suggestions are to see what kinds of charges you can get by fitting to electrostatic potentials, as opposed to the Mulliken charges which are the ones I assume you are reporting. Options for calculating ESP-fitted charges are available in the more recent versions of Ampac and Mopac. Alternatively, can you perform some ab initio calculations (need to be at least at 6-31G* - maybe higher) on a small model compound such as CH3-SO2-NH2 to see what kind of charge is found on the sulfur? I would be interested in seeing the results of any further analysis or prior work that you uncover on this topic posted back to the net. ************************** From: Dan Severance Subject: Re: CCL:Semi-empirical S-charge: 'right' or 'wrong' ? Date: Sun, 26 Jun 94 16:06:46 EDT I don't know if it's an option in MOPAC 93, but try electrostatic potential fit charges; they are MUCH less sensitive to basis set used than Mulliken charges. From: Dan Severance Subject: Re: CCL:Semi-empirical S-charges II Date: Mon, 27 Jun 94 11:38:03 EDT > - Potential derived charges may be the best for modelling purposes and they > may be less basis set dependent. Is this correct, even if the basis set > lacks incorporation of d-orbitals? > I calculated the ESP (Bessler, Merz, Kollman) charges with Mopac93: > Compute the ESP with all 5 basis sets and compare; they are going to be different than the Mulliken charges (in general). We've had surprisingly good luck using CHELPG charges out of G92 (POP=CHELPG,DIPOLE) which constrains the dipole moment to be correct. G92 does have all of the semi empirical basis sets built in to it as well. The other option is to do ab initio (POP=CHELPG or your favorite ESP fit) on this piece just to check the charges for this test molecule. You can always derive the charges on a "per residue" basis approximating that the other pieces of the molecule have a minimal effect on the charges. ************************** Date: Mon, 27 Jun 94 09:34:39 EST From: Dr. Dave Winkler Subject: Re: CCL:Semi-empirical S-charge: 'right' or 'wrong' ? I too have done semiempirical MO calculations on molecules containing sulfur (sulfones and sulfoxides) and have obtained the same behaviour. I would be very interested in what you discover. I had some doubt about the size of the charges but felt that a highly polarizable atom like S, covalently bonded to two oxygens, may have quite a high charge. Please send me any relevant information coming out of this discussion. What about a fixed geometry calculation on something small like DMSO using ab initio methods? ************************** From: "Andrey Bliznyuk" Date: Mon, 27 Jun 1994 17:36:15 Subject: Charges on S It is not clear from your letter, which charges are you going to use. It seems, that you are speaking about Mulliken charges. This charges are not supposed to be used in molecular mechanics calculations, because they do not reproduce electrostatic potential around your molecule. The appropriate way is to use charges generated from electrostatic potential calculation. Most programs can do that. Recently, interesting method have been introduced: G.P. Ford, B. Wang - J. Comp. Chem., 1994, v.15, p.200-207. Ordinary, using such methods you receive hypervalent charges for S / P around 1.8. The problem is that hypervalent S and P are unaccessible. There is a way around: C.I. Bayly, P. Cieplak, W.D. Cornell, P.A. Kollman: J. Phys. Chem., 1993, v.97. p.10269-10280. but, as far as i know, it is not implemented in Ampack/Mopack. Fortunately, for most of the calculations, it is not very important, because the electrostatic potential around molecule is good enough. My experience (for P) is that AM1 charges, derived from electrostatic calculations are good. The Mulliken charges looks ok for me, for example for H2SO4: MNDO = 1.7483 - not parametrizied for hypervalent AM1 = 2.8734 PM3 = 2.5095 MNDO/d = 2.3401 - d orbitals on S. P.S. There are some confusing about Mulliken charges in semiempirical calculations. Here, i am using the standard (in NDO approximation) definition: q(atom a) = Sum(i of a) Pii, where Pii is diagonal elements of density matrix. ************************** Date: Mon, 27 Jun 1994 10:27:50 +0200 From: kit1@mri.ch.cam.ac.uk Subject: sulphur things I just read your email to CCL on sulphur cpds. I tried CHARGE3 in XED (as I expect you have anyway) and found that the charge on the S was +0.2937 . I realise that CHARGE3 is empirical, but MOPAC is semi-empirical. with differences between Hamiltonians. ...stuff deleted... Even when using ab initio ESPs the situation is not clear cut as there is also a basis set dependence. I think you should use the charges you think give the 'best' results, as long as you are consistent in the use of charge models and use a 'standard' of some sort (not much of a problem as there are lots of standards to choose from). I believe the correct international (IUPAC) name for sulphur is sulfur, but I don't think phosphorus was 'changed' for the benefit of 'global communications'. ************************** Date: Mon, 27 Jun 94 10:50:26 +0100 From: "Wojciech Galazka" Subject: Re: CCL:Semi-empirical S-charge: 'right' or 'wrong' ? And did you include d-orbitals to your calculations? Look for SIBIQ program that uses MNDO/d scheme. ************************** Date: Mon, 27 Jun 1994 12:03:24 -0400 (EDT) From: GKING@arserrc.gov Subject: Re: CCL:Semi-empirical S-charge: 'right' or 'wrong' ? I am also interested in the "correct" atomic charges one should use for the sulfone group. I do not have access to programs like G92, so I am interested in your results. Have you performed any G92 calculations on your model molecule CH3-SO2-NH-CH3, or just semi-empirical calculations? A few years ago I found a paper in which the charge of the S in the sulfone group was apparently found to be about 0.9 through some sort of spectroscopy that I am not familiar with. I'm not positive about this number, because the paper was written in Russian (which I do not understand). The number 0.9 appeared in a table in this paper, so I may or may not be interpreting it correctly. I can probably find this paper in my files and provide you with the reference if you are interested. ************************** From: "Christian Boehme" Date: Mon, 27 Jun 1994 18:41:01 MDT Subject: Re: CCL:Semi-empirical S-charge: 'right' or 'wrong' ? To me your results sound reasonable. If you use a semipolar bonding model for this hypervalent compound (which is preferred by a lot of theoretical chemists instead of d-orbital participation), the charge should be around 2.0. I obtained the following Sulfur charges for SF6, using an 6-31G* basis on RHF level : Mulliken : 2.4 Natural Population Analysis : 3.2 Bader s Atoms In Molecules : 4.5 Semipolar bonding suggests a charge around 3.0. So the higher values you obtained may even be the more reasonable ones. Of course you re right in your opinion that atom charges are only a model. I ve recently read a reference which compared different methods to derive such charges. I don t have it at hand but if you re interested, just send me a note. Greetings, ************************** Date: 27 Jun 94 14:21:00 EST From: "DR. LIOTTA" Subject: sulfonamide (repeat message - new address found) I only caught the second message you sent to the CCL but I am very interested in your test model for the sulfonamide bioactive compound. I am trying to model a similar compound, but need to find the v1, v2 and v3 torsional vibration parameters for -S(O2)-N(CH3)-C(sp3)-OH, -S(O2)-N(CH3)-C(sp3)-C(sp2) and -S(O2)-N(CH3)-C(sp3)-C(sp3) Have these been calculated before and if so could you tell me where they are published. Thank you. Veronica Cornel ************************** Date: Tue, 28 Jun 1994 09:52:13 -0400 From: enrico.purisima@BRI.NRC.CA (Enrico Purisima) Subject: CCL:Sulfonamide Two papers that derive force-field parameters for sulfonamides are: Nicholas et al., "A Molecular Mechanics Valence Force Field for Sulfonamides Derived by Ab Initio Methods." J. Phys. Chem. 95:9803-9811 (1991). Bindal et al., "Ab Initio Calculations on N-Methylmethansulfonamide and Methyl Methanesulfonate for the Development of Force Field Parameters and Their Use in the Conformational Analysis of Some Novel Estrogens." JACS 112:7861-7868 (1990). ************************** From: Paulo Henrique Guadanini Subject: S-charges Date: Mon, 27 Jun 1994 17:18:30 -0300 (EST) Hi Moret, I calculated charges for your model compound (CH3-SO2-NH-CH3) using 2 ab initio wave functions (table) . Note that S ESP charge for HF/6-31++G** wave function is 2.5 times smaller than others theoretically derived charges. I included also charges calculated more empirically by the Charge Equilibration method (A.K.Rappe and W.A.Goddard III, J.Phys.Chem. 95,3358(1991)). In this case the S charge have opposite sign. Due to the modest computational costs, you may try to use methods based on the electronegativity equalization approach to calculate charges for the bioactive compounds. See, for example J.Mullay J.Comp.Chem. 9(7), 764(1988) J.Mullay J.Comp.Chem. 12(3), 369(1991) W.J.Mortier, et al J.Am.Chem.Soc. 107,829(1985) W.J.Mortier, et al J.Am.Chem.Soc. 108,4315(1986) T.K.Ghanty and S.K.Ghosh THEOCHEM 276, 83(1992) J.Gasteiger and M.Marsili Tetrahedron 36,3219(1980) A.K.Rappe and W.A.Goddard III, J.Phys.Chem. 95,3358(1991) HF/6-31G HF/6-31G HF/6-31++G** HF/6-31++G** Charge Mulliken CHELPG Mulliken CHELPG Equilibration H .175192 -.063406 .171631 -.083289 .15623 H .052421 -.168608 .006913 -.208642 .08554 H .540226 .371062 .501927 .392285 .26842 H .211525 .067218 .168815 .062701 .11286 C -.949472 -.111049 -.752617 .114410 -.07299 S 1.230307 1.166504 1.433971 .519700** -.09075** N -.514572 -.065378 -.446039 .086295 -.24547 C -.182035 -.092049 -.252464 -.026867 -.20924 H .232512 .007172 .174369 -.029782 .15315 H .243595 .158310 .187150 .151572 .13459 H .255879 .104173 .210553 .095389 .17736 O -.677410 -.694042 -.767149 -.552283 -.21774 O -.618167 -.679908 -.637061 -.521488 -.25194 ************************** From: "Chris L. Waller" Date: Fri, 1 Jul 1994 10:17:12 -0400 Subject: Re: CCL:Semi-empirical S-charges II About sulfonamides: I ran a DFT calculation on your test molecule using a DNP (double numerical with polarization functions) basis set and obtained the following charges: Effective atomic charges from Mulliken populations: O # 1 -0.457 S # 2 0.929 O # 3 -0.455 C # 4 -1.092 N # 5 -0.652 C # 6 -0.906 H # 7 0.362 H # 8 0.388 H # 9 0.395 H # 10 0.460 H # 11 0.354 H # 12 0.337 H # 13 0.336 This was a single point energy calculation on the PM3 optimized structure. ************************** End of the replies. ------------------------------------------------------------------------- E.E. Moret (@more@) E.E.Moret@far.ruu.nl Computational Medicinal Chemistry/Department of Pharmaceutical Chemistry Faculty of Pharmacy/Utrecht University/the Netherlands Telephone (31-30)536979/536958 Facsimile (31-30)516674 ------------------------------------------------------------------------- From hurst@hyper.hyper.com Tue Jul 5 18:50:39 1994 Received: from seraph.uunet.ca for hurst@hyper.hyper.com by www.ccl.net (8.6.9/930601.1506) id RAA19887; Tue, 5 Jul 1994 17:57:41 -0400 Received: from hyper by mail.uunet.ca with UUCP id <91057-1>; Tue, 5 Jul 1994 17:58:10 -0400 Received: by hyper.hyper.com.hyper.com (931110.SGI/890607.SGI) (for ccl.net!chemistry) id AA16946; Tue, 5 Jul 94 17:26:59 -0400 Date: Tue, 5 Jul 1994 17:26:59 -0400 From: hurst@hyper.hyper.com (Graham Hurst) Message-Id: <9407052126.AA16946@hyper.hyper.com.hyper.com> To: chemistry@ccl.net Subject: HyperChem: Working model available on www.ccl.net A demonstration version of HyperChem Release 4 for Windows can be downloaded by anonymous FTP from: Host: www.ccl.net Path: pub/chemistry/software/MS-WINDOWS/hcdemo.zip This demo version is restricted to methanol and the only modelling methods included are the AMBER forcefield (for molecular mechanics) and Extended Huckel (for quantum mechanics). The online help of the full product is included. ------------ Graham Hurst (hurst@hyper.com) Hypercube Inc, 7-419 Phillip St, Waterloo, Ont, Canada N2L 3X2 (519)725-4040 Info requests to: info@hyper.com Support questions to: support@hyper.com Email group: Send "subscribe hyperchem" to hyperchem-request@hyper.com From haney@netcom.com Tue Jul 5 21:50:42 1994 Received: from netcom.com for haney@netcom.com by www.ccl.net (8.6.9/930601.1506) id VAA21421; Tue, 5 Jul 1994 21:31:49 -0400 Received: by netcom.com (8.6.8.1/SMI-4.1/Netcom) id SAA03453; Tue, 5 Jul 1994 18:33:11 -0700 From: haney@netcom.com (Dr. David N. Haney) Message-Id: <199407060133.SAA03453@netcom8.netcom.com> Subject: AMBER USERS To: CHEMISTRY@ccl.net Date: Tue, 5 Jul 1994 18:33:11 -0700 (PDT) X-Mailer: ELM [version 2.4 PL23] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 4534 The following is a summary of responses that I received regarding graphics programs to visualize AMBER results. ORIGINAL POST: I was wondering if anyone has developed a tool to assist in the viewing of AMBER coordinate files. In particular, it seems that someone must have dealt with the potential of converting AMBER's coordinate files mdcrd and mincor for MINMD to a file type that could be read by Sybyl, Quanta or InsightII. As far as I can tell BABEL cannot deal with this problem. Abbreviated responses: ----------------------- From: vepa@rox.mel.dbe.csiro.au (Vidana C. Epa) The ANAL module of AMBER v.4.0 can convert 'mincor' files into PDB format, while the CARNAL module (not yet a standard AMBER module) can convert 'mdcrd' files into PDB format. Once it's in PDB format, of course, it may be viewed with any mol. modelling graphical interface. From: David Case The usual procedure is to create "PDB" format files, which the programs you mention above can read. You can do this through ANAL, or with the program ambpdb. I usually use the latter, but don't remember if it is in the 4.0 distribution or not...it's certainly in 4.1, probably in src/etc. Or I can mail you a copy if you like. From: Jeff Dyason I believe that you can convert the amber trajectory files into a whole heap of pdb files (i.e. file1.pdb, file2.pdb, .... fileN.pdb), these can then be converted to at least an InsightII .arc file by a bcl macro, which I distributed via the dibug mailing list last year. The macro is not fool proof, because of the naming of some atoms, but this is fairly easily tailored to a particular system. We generally use it here to analyse x-plor structures derived from nmr data, although I think someone has used it for amber files. If you want a copy of the macro or any further information just e-mail me. From: charlie@iris5.icr.ac.uk (Charles Laughton) Here we use Terry Lybrand's program MD-Display to view our AMBER md snapshot files. It works fine for us, though it may not offer all the functionality that Sybyl, Quanta or InsightII might give you. I'm sorry, I can't find an e-mail address for Terry for you (but he's at the University of Washington, Seattle). From: ross@cgl.ucsf.edu (Bill Ross ) If those progs read pdb, carnal will do the job for mdcrd; pdbgen & carnal do it for mincor.. the other progs' user communities probably have stuff too; there is a parm file routine in carnal that can be adapted to get the bond info & atom types for writing converted files. From: david@auvergne.cbs.univ-montp1.fr (David Cregut) We modified the PDBGEN utility from AMBER 4.0 in order to read mdcrd and parm files from AMBER and to write a file to the Insight II archive format. The trajectory can then be viewed using the analysis module of Insight II. From: K Bryson A little program called 'groch' in the 'util' directory of Quanta can be used to convert mdcrd files from amber to DCD animation files for Quanta. You also need to 'Import' a pdb file from amber to Quanta to get the topology of the structure into quanta. ( Originally groch was for GROMOS mdcrd file to Quanta DCD conversion, but Amber hasn't changed the format of this output file from the original GROMOS standard. ) From: mitchell@bdrc.bd.com (Mike Mitchell) There are already Sybyl Programming Language (SPL) and C language utilies to convert AMBER trajectory data to a Sybyl .his file. Look in $TA_ROOT/spl and get the ambertosybyl.spl script. From: Pat Walters I'm the author of Babel. If you send me samples and specifications for some of these file formats I'd be glad to add them to Babel. Actually I have an AMBER 4.0 manual so if the specs are in the manual all I'll probably need are a few sample files. It usually takes me me very little time to do this. From: "Jeffrey P. Jones" AMBER files can be converted to SYBYL readable files by the macro ambertosybyl. SYBYL> take $TA_ROOT/tables/sample.macros SYBYL> ambertosybyl Answer the questions and wait a long time for a history file. -- ************** David N. Haney, Ph.D. **************** * Haney Associates Phone - 619-566-1127 * * 12010 Medoc Ln. * * San Diego, CA 92131 Fax - 619-586-1481 * ************** Email - haney@netcom.com ***************