Show us that part of your topology. When you used ffamberports have you renamed the CYS to CYS2?
Oliver On 20 January 2011 09:23, <parthi...@ncbs.res.in> wrote: > > Message: 5 > > Date: Wed, 19 Jan 2011 08:37:20 -0500 > > From: "Justin A. Lemkul" <jalem...@vt.edu> > > Subject: Re: [gmx-users] Re: Problem in Disulfide Bond > > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > > Message-ID: <4d36e910.6030...@vt.edu> > > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > > > > > parthi...@ncbs.res.in wrote: > >> Hi > >> > >> I am using a dimer for my simulation system which is connected by 2 > >> disulfide bonds. > >> After energy minimization for even few cycles, the disulfide bond breaks > >> which is not expected. > > > > Bonds do not break in classical molecular mechanics. One of two things > is > > happening: > > > > 1. There was never a bond to begin with (check your topology) > There do a bond exists. > > 2. The bond is highly strained, in which case something is wrong with > your > > structure. > > > >> i have applied amber99 force field and prepared the system. while i > >> tried > >> with another force field in Gromacs which did not worked at all. > > > > What does that mean? What failed? > As said previously the bond is strained only after pdb2gmx itself. is > there any other way to fix it. > > but in gendral the molecule is free from strains. > > > >> also i have tried by editing specbond.dat as well but of no use. > > > > In what way? Have you seen the information at: > > > > http://www.gromacs.org/Documentation/File_Formats/specbond.dat > > > > i tried to alter the distance of cys bond length by +/-. > reg, > Parthi. > > > -Justin > > > >> can any one share/discuss some ideas how to fix this. > >> > >> reg's, > >> Parthiban. > >> > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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