On 01/20/11, parthi...@ncbs.res.in wrote: > > Message: 3 > > Date: Thu, 20 Jan 2011 09:30:00 +0000 > > From: Oliver Grant <olivercgr...@gmail.com> > > Subject: Re: [gmx-users] Re: Problem in Disulfide Bond > > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > > Message-ID: > > <AANLkTin5r=+mn5edW=zqdhru8facoqedovixc8x28...@mail.gmail.com> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Show us that part of your topology. When you used ffamberports have you > > renamed the CYS to CYS2? > > > > Oliver > > > > could you explain this in detail where this change have to done.? i can > check again. > > > ------------------------------ > > > > Message: 4 > > Date: Thu, 20 Jan 2011 20:54:39 +1100 > > From: Mark Abraham <mark.abra...@anu.edu.au> > > Subject: Re: [gmx-users] Re: Problem in Disulfide Bond > > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > > Message-ID: <7690be842aff.4d38a...@anu.edu.au> > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > > >> > 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. > >> > > > > So you can see in your [bonds] section an entry for the two atom numbers? > > I cant see any corresponding entry with res.to CYS residues. >
So you didn't make a bond. Anything you saw in pymol or vmd is irrelevant. They didn't read your .top file and that's what counts. You need to call pdb2gmx properly. Mark > > > > > >> > >> > 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. > >> > > > > Previously you said the bond was strained after EM. pdb2gmx is not capable > > of straining a bond. > > > > Be sure you are not looking at "bonds" generated via heuristics in some > > visualization program. If pdb2gmx is generating a disulfide bond, it will > > say so in the standard output, and you will be able to find it in the > > [bonds] section. Otherwise, there is no bond. > > > > Mark > > > > I used pymol and vmd to visualize this > > Thanks > 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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