[gmx-users] Add missing residue

[Nizar Masbukhin]

That happens when amber forcefield is used, doesnt it?. I'm using Gromos96
54a7 ff.

On Sun, Sep 28, 2014 at 10:02 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> 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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-- 
Thanks
My Best Regards, Nizar
Medical Faculty of Brawijaya University