From chemistry-request $#at#$ server.ccl.net Tue Oct 12 15:27:34 1999 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA04800 for ; Tue, 12 Oct 1999 15:27:34 -0400 Received: from bioc1.msi.com (bioc1.msi.com [146.202.0.2]) by ccl.net (8.8.6/8.8.6/OSC 1.1) with ESMTP id PAA26250 for ; Tue, 12 Oct 1999 15:22:24 -0400 (EDT) Received: (from daemon- at -localhost) by bioc1.msi.com (980427.SGI.8.8.8/970903.SGI.AUTOCF) id MAA15833 for ; Tue, 12 Oct 1999 12:22:45 -0700 (PDT) Received: from dxg-pc.msi.com(146.202.11.19) by bioc1.msi.com via smap (V2.0) id xma015827; Tue, 12 Oct 99 12:22:35 -0700 Message-Id: <3.0.32.19991012121824.00938d20 |-at-| 146.202.6.130> X-Sender: dgregory*- at -*146.202.6.130 X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Tue, 12 Oct 1999 12:18:24 -0700 To: chemistry $#at#$ ccl.net (Comp. Chem. List) From: Don Gregory Subject: Re: [charmm-bbs] H-bond parameters (2) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Hi Lesley, I'm glad you asked these two questions, because they point out some important aspects I was trying to make in my earlier response. Empirical force fields can *only* calculate those energy term they are parameterized for, so if you are using a force-field that wasn't parameterized using an explicit H-Bond term, it would be an inappropriate question to ask "what is the H-Bond component". To ask this question, you'd have to use a force-field that was parameterized using explicit H-Bonding terms (which would no doubt have other parameters different [e.g. electrostatics and vdW]) You can 'approximate' the strength of the H-Bonds by 'turning them on' (i.e. incr. cuthb) but these numbers should *not* be relied upon too greatly, since, again, those values were not used in the force-field optimization. They are probably hold-overs from earlier optimizations when they were included explicitly. As for 'what do you do when there are no H-Bond terms in the force-field' (even if you are using a field that has explicit H-Bond terms); the answer there is the same as any 'missing parameter' problem, i.e. you'd need to search the literature to see if anyone has optimized such a parameter *using* the same force-field you are using. The script I provided still works with a Cys present, but you're right, since there are not terms to calculate, one cannot even analyze for H-Bond geometries (which is the recommended use of the H-Bond commands I gave; also Lennart Nilsson reminded us of the "coor hbond" command which helps with analysis w/o the use of the force-field parameters). DG At 04:25 PM 10/11/1999 +0100, you wrote: >Thank you all for your help regarding my recent question on H-bond >parameters. Following on from everything that has been said I would like >to ask two more questions: > >(1) If hydrogen bonding is implicit in electrostatics and vdW terms, how >do you analyse the energy term to find the contribution to energy which >is due to hydrogen bonding? I assume this is a valid occasion for using >HBONDS > >(2) If you determine the energy due to hydrogen bonds using HBONDS CUTHB >4.5 (for example), how do you account for sulfur containing systems, >particularly cysteine residues, when sulfur is not parameterised in the >HBOND section of the parameter file? > >If you run the script that Don Gregory sent to the list, but replace one >of the residues with CYS this adapted script falls over because there >are no hydrogen bond parameters. > >Thanks again for your help so far. Look forward to hearing from you >again. >Lesley Dr. Don Gregory (dgregory "-at-" msi.com) Asia Pacific Science Liaison Molecular Simulations Inc. 9685 Scranton Rd. San Diego, CA 92121 (619) 799-5331 http://www.msi.com