[gmx-users] Add missing residue

[Johnny Lu]

Sometimes the forcefield can not directly use the residue names of a pdb
file.
In Amber forcefield, a glycine at c-terminal should be 'CGLY' instead of
just GLY.
Similarly, there is 'NGLY'. And histidine of different protonation states
have different names.
Cysteine with and without disulfide bond can have different names.
Sometimes residues in the pdb file can have multiple positions.

On Sun, Sep 28, 2014 at 10:45 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> There are some suggestions at
> http://www.gromacs.org/Documentation/File_Formats/Coordinate_File
>
> Mark
>
> On Sun, Sep 28, 2014 at 4:35 PM, Nizar Masbukhin <nizar.fkub08 at gmail.com>
> wrote:
>
> > Dear users,
> >
> > I'm going to simulate a protein. On the pdb file contents, it's said that
> > this protein has two chains, and missing residues and atoms. when I try
> to
> > pdb2gmx, the error messages occured. It seemed due tue the missing
> residue
> > so that i got the message error.
> > My question is: How can I add missing resiudes and atoms to the pdb files
> > so that i can use it?
> >
> > Thanks
> > --
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