> 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. > > >> >> > 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
