Hi All, I did not receive a response yet for my question below, so I am submitting it once again.
Thanks again in advance for your help. Darrell On 4/12/2009, "<darre...@localhost>" <> wrote: >Hi All, >Yes, indeed, the topology file does have the #include statement. Here is >an extract from the topology file: >*************************************************************************** >; Include forcefield parameters >#include "ffoplsaa.itp" > >[ moleculetype ] >; Name nrexcl >ICE 3 > >[ atoms ] >; nr type resnr residue atom cgnr charge mass >typeB chargeB massB > 1 opls_145 1 Grph CA 1 0 12.011 ; >qtot 0 >*************************************************************************** >Please advise what may be the problem. > >Thanks. > >Darrell > >>Date: Sun, 12 Apr 2009 07:34:46 +0200 >>From: David van der Spoel <[email protected]> >>Subject: Re: [gmx-users] Missing VdW Parameters >>To: Discussion list for GROMACS users <[email protected]> >>Message-ID: <[email protected]> >>Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >>[email protected] wrote: >>> Dear All, >>> I successfully ran the x2top command (x2top -ff select -f graphene_nm.gro >>> -o graphene_nm.top) and generated a topology using ffoplsaa, but my >>> topology is missing VdW parameters, which I thought should be appearing >>> in the [ pairs ] section of the topology file. I thought that x2top >>> would use the VdW parameters in ffoplsaanb.itp to populate the [ pairs ] >>> section of the topology file. But this appears not to be the case. >>> Please advise what may be the problem. >>> >>> To help diagnose this problem, I am including a portion of the .gro file, >>> the relevant section of the .n2t file, and a portion of the [ pairs ] >>> section from the generated topology file. >> >>is there a >>#include "ffoplsaa.itp" >>statement in the top file ? >> >> >>> >>> selection from .gro file: >>> 2Grph C 1 0.000 0.000 0.000 0.0000 0.0000 0.0000 >>> 2Grph C 2 0.071 -0.123 0.000 0.0000 0.0000 0.0000 >>> 2Grph C 3 0.071 0.123 0.000 0.0000 0.0000 0.0000 >>> >>> relevant section of .n2t file: >>> C opls_145 0 12.011 3 C 0.140 C 0.140 C 0.140 >>> C opls_145 -0.06 12.011 3 C 0.140 C 0.140 H 0.108 >>> C opls_145 -0.12 12.011 3 C 0.140 H 0.108 H 0.108 >>> H opls_146 0.06 1.008 1 C 0.108 >>> >>> selection from generated topology file: >>> [ pairs ] >>> ; ai aj funct c0 c1 c2 c3 >>> 1 11 1 >>> 1 12 1 >>> 1 13 1 >>> 1 14 1 >>> >>> Much thanks in advance. >>> >>> Darrell >>> _______________________________________________ >>> gmx-users mailing list [email protected] >>> http://www.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at http://www.gromacs.org/search before posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to [email protected]. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >>-- >>David van der Spoel, Ph.D., Professor of Biology >>Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. >>Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. >>[email protected] [email protected] http://folding.bmc.uu.se >> >> >>------------------------------ _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
