From chemistry-request@server.ccl.net Wed Apr 11 17:52:43 2001 Received: from matavnet.hu ([195.228.240.10]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f3BLqg014711 for ; Wed, 11 Apr 2001 17:52:42 -0400 Received: (qmail 14122 invoked from network); 11 Apr 2001 23:52:41 +0200 Received: from line-141-26.dial.matav.net (HELO cthulhu) (145.236.141.26) by mail.matavnet.hu with SMTP; 11 Apr 2001 23:52:41 +0200 Message-ID: <001101c0c2d2$1e6aa480$0200a8c0@cthulhu> From: "Tamas Gunda" To: "Leif Laaksonen" , References: Subject: Re: CCL:PDB file format Date: Wed, 11 Apr 2001 23:55:26 +0200 Organization: University of Debrecen MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 ----- Original Message ----- > > Hi, > > According to the PDB file format defined in: > > http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html > > the ATOM/HETATM record reserves only 4 digits to the residue > sequence number (max 9999). > > 23 - 26 Integer resSeq Residue sequence number. > > However, in some systems we already have residue sequence numbers > above 9999. Specially in MD simulations including water. What do > you people use to solve this problem because column position 27 is > already reserved? > > 27 AChar iCode Code for insertion of > residues. > > Regards, > > -leif laaksonen > Leif, Well, that's a limitation in pdb format. An alternative could be the use of mmCIF format, (macromolecular CIF) which is a kind of "translation" of PDB format to the CIF one. It uses tag-defined definitions and not fixed format: loop_ _atom_site.label_seq_id _atom_site.group_PDB _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.auth_seq_id _atom_site.label_alt_id _atom_site.cartn_x _atom_site.cartn_y _atom_site.cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.footnote_id _atom_site.label_entity_id _atom_site.id 1 ATOM N N GLY A 1 . -8.863 16.944 14.289 1.00 21.88 1 1 1 1 ATOM C CA GLY A 1 . -9.929 17.026 13.244 1.00 22.85 1 1 2 1 ATOM C C GLY A 1 . -10.051 15.625 12.618 1.00 43.92 1 1 3 1 ATOM O O GLY A 1 . -9.782 14.728 13.407 1.00 25.22 1 1 4 2 ATOM N N ILE A 2 . -10.333 15.531 11.332 1.00 26.28 1 1 5 etc See e.g. http://www.iucr.org/iucr-top/cif/mmcif/workshop/ or http://www.sdsc.edu/pb/cif/tutorial_mm.html As there is no such rule that the residue numbering must be consecutively 1,2...N, and pdb files can be found with disordered numbering, most programs do not input the residue seq. numbers themselves, but count the residues by following the changes of the numbers. In this case after 9999 simply start over from 1 again. But this is, of course, only an in-house solution, if all softwares in question support it. best regards Tamas Dr Tamas E. Gunda Research Group for Antibiotics University of Debrecen H-4010 Debrecen, POBox 36 Hungary e-mail: tamasgunda@tigris.klte.hu http://dragon.klte.hu/~gundat From chemistry-request@server.ccl.net Thu Apr 12 11:03:12 2001 Received: from physics.msuiit.edu.ph ([202.78.82.11]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f3CF33024813 for ; Thu, 12 Apr 2001 11:03:07 -0400 Received: by physics.msuiit.edu.ph (Postfix, from userid 701) id EDFFE6312A; Thu, 12 Apr 2001 21:25:56 +0800 (PHT) Received: from localhost (localhost [127.0.0.1]) by physics.msuiit.edu.ph (Postfix) with ESMTP id DDDD2579AA for ; Thu, 12 Apr 2001 21:25:56 +0800 (PHT) Date: Thu, 12 Apr 2001 21:25:56 +0800 (PHT) From: Arnold Alguno To: Subject: Gaussian to Gamess format Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII hello CCLers, may i know what is the equivalent of 6-31+G and 6-31G* in Gaussian Gbasis to Gamess Gbasis? Furthermore, what is the equivalent of CEP-31, CEP-31+G and CEP-31G* in Guassian Gbasis to Gamess Gbasis? thanks a lot. -- _________ Very truly yours, ARNOLD C. ALGUNO IITHEP, Department of Physics MSU-IIT, Iligan City Philippines alguno@physics.msuiit.edu.ph Mobile Phone No.:+63-919-427-8205 From chemistry-request@server.ccl.net Thu Apr 12 11:00:42 2001 Received: from admin.cnrs-orleans.fr ([163.9.1.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f3CF0f024775 for ; Thu, 12 Apr 2001 11:00:41 -0400 Received: from chinon.cnrs-orleans.fr (chinon.cnrs-orleans.fr [163.9.6.107]) by admin.cnrs-orleans.fr (8.9.1a/jtpda-5.3.2) with ESMTP id RAA25304 ; Thu, 12 Apr 2001 17:00:36 +0200 (MET DST) Received: (from hinsen@localhost) by chinon.cnrs-orleans.fr (8.9.3/8.9.3) id RAA03888; Thu, 12 Apr 2001 17:01:04 +0200 Date: Thu, 12 Apr 2001 17:01:04 +0200 Message-Id: <200104121501.RAA03888@chinon.cnrs-orleans.fr> X-Authentication-Warning: chinon.cnrs-orleans.fr: hinsen set sender to hinsen@cnrs-orleans.fr using -f From: Konrad Hinsen To: Leif.Laaksonen@csc.fi CC: chemistry@ccl.net In-reply-to: Subject: Re: CCL:PDB file format References: > However, in some systems we already have residue sequence numbers > above 9999. Specially in MD simulations including water. What do > you people use to solve this problem because column position 27 is > already reserved? Here is how I handle residue sequence numbers in the Molecular Modelling Toolkit (MMTK): For output: residue numbers are written module 10000. In most cases, i.e. unless application programs supply their own residue numbers, this means that 9999 is followed by 0. For input: MMTK requires only that two subsequent residues have different residue numbers, the value is not used otherwise (but stored internally so that application programs can use it if they see a need). -- ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsen@cnrs-orleans.fr Centre de Biophysique Moleculaire (CNRS) | Tel.: +33-2.38.25.56.24 Rue Charles Sadron | Fax: +33-2.38.63.15.17 45071 Orleans Cedex 2 | Deutsch/Esperanto/English/ France | Nederlands/Francais ------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Thu Apr 12 11:23:09 2001 Received: from narnia4.rutgers.edu ([165.230.180.169]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f3CFN9025051 for ; Thu, 12 Apr 2001 11:23:09 -0400 Received: from eden.rutgers.edu (molly.envsci.rutgers.edu [165.230.5.148]) by narnia4.rutgers.edu (8.8.8/8.8.8) with ESMTP id LAA19536 for ; Thu, 12 Apr 2001 11:23:08 -0400 (EDT) Message-ID: <3AD5C940.D1955BDF@eden.rutgers.edu> Date: Thu, 12 Apr 2001 11:26:57 -0400 From: "Mary O'Connor" X-Mailer: Mozilla 4.08 [en] (Win98; I) MIME-Version: 1.0 To: chemistry@ccl.net Subject: Summary Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Thank-you for your responses to my question regarding self-learning of docking molecules. Resources are: 1.) The Scripps home page for Autodock 2.) Two books: Molecular Mechanics and Conformational Analysis in Drug Design by Gyorgy M. Keseru and Istvan Kolossvary, Blackwell Sciences, 1998. Guidebook on Molecular Modelling in Drug Design, edited by N. Claude Cohen, Academic Press, 1996. 3.) A webpage robotics.stanford.edu/~latombe/papers/icra01/final.PDF. Thank you all very much. Mary O'Connor Rutgers University New Brunswick, NJ From chemistry-request@server.ccl.net Thu Apr 12 12:26:54 2001 Received: from matavnet.hu ([195.228.240.10]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f3CGQr025763 for ; Thu, 12 Apr 2001 12:26:53 -0400 Received: (qmail 25310 invoked from network); 12 Apr 2001 18:26:51 +0200 Received: from line-141-235.dial.matav.net (HELO cthulhu) (145.236.141.235) by mail.matavnet.hu with SMTP; 12 Apr 2001 18:26:52 +0200 Message-ID: <001401c0c36d$c4a3e1e0$0200a8c0@cthulhu> From: "Tamas Gunda" To: "Leif Laaksonen" , References: Subject: Re: CCL:PDB file format 2 Date: Thu, 12 Apr 2001 18:29:36 +0200 Organization: University of Debrecen MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Leif, Yesterday after having posted my answer it came into my mind that in the PDB files the residue sequence numbering can be restarted in every chains. I don't know the exact structure of your file, but a solution could be that simply & formally split for example the water stuff into several chains, in each one the residue numbering starting from 1. If the file creator program was made by you, it is easy to modify the output routine. best regards Tamas Dr Tamas E. Gunda Research for Antibiotics University of Debrecen H-4010 Debrecen, POBox 36 Hungary e-mail: tamasgunda@tigris.klte.hu http://dragon.klte.hu/~gundat ----- Original Message ----- From: "Leif Laaksonen" To: "Chemistry@Ccl. Net" Sent: Wednesday, April 11, 2001 9:45 AM Subject: CCL:PDB file format >> >> Hi, >> >> According to the PDB file format defined in: >> >> http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html >> >> the ATOM/HETATM record reserves only 4 digits to the residue >> sequence number (max 9999). >> >> 23 - 26 Integer resSeq Residue sequence number. >> >> However, in some systems we already have residue sequence numbers >> above 9999. Specially in MD simulations including water. What do >> you people use to solve this problem because column position 27 is >> already reserved? >> >>27 AChar iCode Code for insertion of >> residues. >> >> Regards, >> >> -leif laaksonen >> >Leif, >Well, that's a limitation in pdb format. An alternative could be the use of mmCIF format, >(macromolecular CIF) which is a kind of "translation" of PDB format to the CIF one. It uses >tag-defined definitions and not fixed format: >loop_ >_atom_site.label_seq_id >_atom_site.group_PDB >_atom_site.type_symbol >_atom_site.label_atom_id >_atom_site.label_comp_id >_atom_site.label_asym_id >_atom_site.auth_seq_id >_atom_site.label_alt_id >_atom_site.cartn_x >_atom_site.cartn_y >_atom_site.cartn_z >_atom_site.occupancy >_atom_site.B_iso_or_equiv >_atom_site.footnote_id >_atom_site.label_entity_id >_atom_site.id >1 ATOM N N GLY A 1 . -8.863 16.944 14.289 1.00 21.88 1 11 >1 ATOM C CA GLY A 1 . -9.929 17.026 13.244 1.00 22.85 1 12 >1 ATOM C C GLY A 1 . -10.051 15.625 12.618 1.00 43.92 1 13 >1 ATOM O O GLY A 1 . -9.782 14.728 13.407 1.00 25.22 1 14 >2 ATOM N N ILE A 2 . -10.333 15.531 11.332 1.00 26.28 1 15 >etc >See e.g. http://www.iucr.org/iucr-top/cif/mmcif/workshop/ >or http://www.sdsc.edu/pb/cif/tutorial_mm.html >As there is no such rule that the residue numbering must be consecutively >1,2...N, and pdb files can be >found with disordered numbering, most programs do not input the residue seq. >numbers themselves, but count the residues by following the changes of the >numbers. In this case after 9999 simply start over from 1 again. But this >is, of course, only an in-house solution, if all softwares in question >support it. >best regards >Tamas From chemistry-request@server.ccl.net Thu Apr 12 16:30:58 2001 Received: from ivory.trentu.ca ([192.75.12.103]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f3CKUw028681 for ; Thu, 12 Apr 2001 16:30:58 -0400 Received: from trentu.ca ([204.225.13.50]) by trentu.ca (PMDF V5.2-32 #29543) with ESMTP id <01K2BHJNTSK6005X28@trentu.ca> for chemistry@ccl.net; Thu, 12 Apr 2001 16:29:54 EDT Date: Thu, 12 Apr 2001 16:35:39 -0400 From: elewars Subject: POTENTAL ENERGY SURFACE, CONCEPT To: chemistry@ccl.net Message-id: <3AD6119B.7836631C@trentu.ca> MIME-version: 1.0 X-Mailer: Mozilla 4.7 [en] (WinNT; I) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en 2001 April 12, Thursday In his textbook "Physical Chemistry", 4th Ed., 1972, page 377, Walter J. Moore (author of the definitive biography of Erwin Schroedinger, 1989) says that "The idea that a chemical reaction can be represented by [a potential energy surface] was suggested by Marcelin in 1915..." and gives this reference: Marcelin, Ann. Phys., 3, 158 (1915). (1) Does anyone know who Marcelin was, and his initial(s) (A. Marcelin, B. Marcelin, etc)? (2) If someone could email or FAX me the title and author part of the paper above I would very much appreciate it. Is _Ann. Phys._ of 1915 Annalen der Physik or Annales de Physique, or what? Thank you. E. Lewars FAX (705) 748-1625 E.Lewars ===== From chemistry-request@server.ccl.net Thu Apr 12 20:08:41 2001 Received: from mail.shcnc.ac.cn ([202.127.16.22]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f3D08eC03347 for ; Thu, 12 Apr 2001 20:08:40 -0400 Received: from pc7 ([202.127.19.247]) by mail.shcnc.ac.cn (8.9.3/8.9.3) with SMTP id JAA08116 for ; Fri, 13 Apr 2001 09:01:42 +0800 (CST) Message-Id: <200104130101.JAA08116@mail.shcnc.ac.cn> Date: Mon, 16 Apr 2001 8:54:4 +0800 From: shen Lingling To: "chemistry@ccl.net" Subject: problem with xplo2d X-mailer: FoxMail 3.0 beta 2 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Hi, I have one question about xplo2d, which is xplor compatible software to make small molecular force field. My question is, after all parameters in parameter file and topology file well done, did it means all infomation such as aromatic ring plane are defined? I got a force field which keep the structure well after minimization, but the aromatic ring was distorted when I perform a molecular dynamic simulation to it. I wonder it is because my force field did not restrain all aromatic atoms to a plane. If so, what else I can do? Any suggestion is welcome! Lingling Shen