From chemistry-request@server.ccl.net Sat May 27 13:27:26 2000 Received: from tisch.mail.mindspring.net (tisch.mail.mindspring.net [207.69.200.157]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA20103 for ; Sat, 27 May 2000 13:27:25 -0400 Received: from josiah ([209.138.214.74]) by tisch.mail.mindspring.net (8.9.3/8.8.5) with ESMTP id NAA10449; Sat, 27 May 2000 13:27:07 -0400 (EDT) Message-ID: <000601bfc801$3c6c0d60$4ad68ad1@josiah.daylight.com> From: "Andrew Dalke" To: "Keith Refson" , "CCL, Computational Chemistry List" Subject: Re: CCL:PDB format with 100000 atoms Date: Sat, 27 May 2000 11:30:19 -0600 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 4.72.3155.0 X-MimeOLE: Produced By Microsoft MimeOLE V4.72.3155.0 Keith Refson asked CCL: >According to the Brookhaven PDB format website it seems that only a 5 >digit field is allowed for the atom sequence number, so there is no >way of generating a correct PDB file containing 100000 atoms or more. > >Has anyone else come up against this limit and found any workaround? XPLOR uses a base-36 digit for the first field (that is, 99998 99999 A0000 A0001 ... Z9999 ). This takes you up to 36,000 atoms. This isn't legal, according to the PDB format. There are some submitted structures with over 100,000 atoms. In that case, the PDB splits the submission into two parts. For example and 1BGL and 1BGM are parts of the same structure - 66344 and 66310 http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1BGL http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1BGM I personally believe software reading a PDB file should ignore the atom index fields. The ones from the PDB always have numbers starting >from 1 and never have gaps. I've never seen files elsewhere which encoded information in those numbers. (There can be different numbering schemes as when creating the full structure from a monomer, but that scheme exists only long enough to renumber it in the proper form.) For output, I've usually extended XPLOR's notation, and let the first character of the serial number go to 'A' after '9'. I then continue the ASCII sequence after 'Z', so '[', '\', ']', ... . That gives up to 2 million atoms, though after that it loops back to 0 and starts generating '\000' (C's end-of-string character) and '\n' (newline) which would affect parsing. Something will have to be done when we start manipulating 2 million atom structures but the most I've done to date is a million atoms, for a software stress test. Andrew dalke@acm.org From chemistry-request@server.ccl.net Sun May 28 01:35:02 2000 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA22727 for ; Sun, 28 May 2000 01:35:02 -0400 Received: from arlen.ccl.net (arlen.ccl.net [192.148.249.10]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id BAA23998; Sun, 28 May 2000 01:34:27 -0400 (EDT) Date: Sun, 28 May 2000 01:34:29 -0400 (EDT) From: Jan Labanowski To: quanta@chem.unipune.ernet.in cc: Jan Labanowski , CHEMISTRY@server.ccl.net Subject: Re: CCL:Address Please !!! In-Reply-To: <200005271946.BAA00913@chem.unipune.ernet.in> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL, This is just to remind CCL subscribers that posting address inquires is discouraged at CCL. Please consult the rules of CCL available at: http://www.ccl.net/aboutccl >From what I know, Prof. Friedrich Cramer may be retired at this moment (he is like 77 years old), though he was quite active last year. He was a director of the Max-Planck Institute for Experimental Medicine in Goettingen, and has many honorary professorships and memberships all around he world. See e.g.: http://www.uni-kassel.de/fb19/fsr/ring/cramer.html For his whereabouts check: http://www.mpiem.gwdg.de/index.html Prof. Dr. Friedrich Cramer Adresse: Hermann-Rein-Str. 3 37075 Goetingen Telefon: 0551-3899-115 Telefax: 0551-3899-284 E-Mail: cramer@.em.mpg.de On Sun, 28 May 2000 quanta@chem.unipune.ernet.in wrote: > May 28, 2000 > > Can anyone please tell me the address of Dr. friedrich Cramer, one of the > contributor of the following book. > > The Lock-and-Key Principle, Vol. 1, > The State of the Art--100 Years On > Edited by: Jean-Paul Behr (Univ. Louis Pasteur de Strasbourg, Illkirch, France) > > > And the article is: > Emil Fischer's Lock-and-Key Hypothesis After 100 Years_Towards a Supracellular Chemistry (F. Cramer). > > Thanks in advance. > ANANT Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 Ohio Supercomputer Center | Internet: jkl@ccl.net 1224 Kinnear Rd, | http://www.ccl.net/chemistry.html Columbus, OH 43212-1163 | http://www.ccl.net/ From chemistry-request@server.ccl.net Sun May 28 14:39:37 2000 Received: from mailbox.syr.edu (root@mailbox.syr.edu [128.230.18.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA26652 for ; Sun, 28 May 2000 14:39:36 -0400 Received: from syr.edu (curie.syr.edu [128.230.187.116]) by mailbox.syr.edu (8.9.2/8.9.2) with ESMTP id OAA02288 for ; Sun, 28 May 2000 14:39:36 -0400 (EDT) Sender: desingh@mailbox.syr.edu Message-ID: <39316915.3CEC931@syr.edu> Date: Sun, 28 May 2000 14:44:37 -0400 From: Deepak Singh Organization: Birge Group, Dept. Of Chemistry, Syracuse Univ. X-Mailer: Mozilla 4.61C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: Computational Chemistry List Subject: qmmm simulations Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello I have a question related to QMMM methods ? Everytime I do a study on a protein,I use a separate RTF for a qmmm job and a separate one for a pure MM job. If I use the qmmm topology (with a link atom defined for a particular residue) how will it affect a pure MM simulation, i.e. one in which I do not define a QM region but use a topology with an extra link atom? It has mass so it should be part of a lot of energy terms. It has no charge so it should not create any trouble there. I am just curious about whether people have tried that and if they see any results that might be "interesting". Deepak