[gmx-users] pdb2gmx

[Chris Gaughan]

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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