[gmx-users] pdb2gmx

[Pradeep Kota]

Thanks chris,
it worked..:)
thanks others for your inputs..:)

On 12/14/05, Chris Gaughan <clgaughan68 at yahoo.com> wrote:
>
> Can you give each chain different lables using -label
> in editconf? That may well be the problem. Also,
> gromacs doesn't seem to recognize Ter cards for some
> reason. I had the same problem when simulating
> dimerization of two peptide chains. It treated them as
> one single unit. I just used the -label option for
> each pdb and then concatenated.
>
> --- Pradeep Kota <kotanmd at gmail.com> wrote:
>
> > thanks Mr.Larsson..
> > but i checked the pdb file for such errors and
> > couldnt find any. there are
> > four chains in my pdb file. and each chain is named
> > separately and all
> > chains are separated by ter tags properly. is there
> > any other possibility of
> > this error?
> > thanks again..
> > reg.
> > tand
> >
> >
> > On 12/14/05, Per Larsson <per.larsson at sbc.su.se>
> > wrote:
> > >
> > > Check your pdb-file using a text editor of some
> > sort.
> > > Probably you have the same chainID for some
> > residues with another (or
> > > possibly none) chain ID in between. All residues
> > belonging to the same
> > > chain need to have the same chain identifier.
> > >
> > > Regards
> > > /Per
> > >
> > >
> > > Pradeep Kota wrote:
> > >
> > > > hi
> > > > i'm new to gromacs
> > > > pdb2gmx gives an error
> > > > i have a two subunit protein
> > > > pdb2gmx says
> > > > fatal error : use of same chain marker A in non
> > sequential residues
> > > > and it displays the atom number also.
> > > > i checked the pdb file and the two domains are
> > file and i visualised
> > > > them using rasmol. wat do i do?
> > > > thanks for any help
> > > > tand
> > > >
> > >
> >
> >------------------------------------------------------------------------
> > > >
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> > >
> > > --
> > > ********************************
> > > Per Larsson
> > > PhD Student
> > > Stockholm Bioinformatics Center
> > > +46 (0) 8 55378577
> > > +46 (0) 733 461467
> > > per.larsson at sbc.su.se
> > > www.sbc.su.se
> > >
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