[gmx-users] Missing Residues of PDB file

[rama david]

Dear Neha,
       the question depend on which residue is missing??
Is the residue is from middle or from end that is important.
If end residue is missing then no issue. but middle residue  is problematic.
you can model the protein and then align it with pymol align command or any
other visualizing software.


With beat regards,
Rama david.



On Mon, Aug 25, 2014 at 11:01 AM, RINU KHATTRI <nickname.mittu at gmail.com>
wrote:

> use -missing in last of command pdb2gmx
>
> On Mon, Aug 25, 2014 at 10:54 AM, neha bharti <nehabharty123 at gmail.com>
> wrote:
> > Hello All
> >
> > I am performing Molecular dynamics simulation of protein-ligand complex
> > using charmm36 force field in popc lipid.
> >
> > I downloaded the protein ligand complex pdb file. And as mentioned in
> > Justin A. Lemkul protein-ligand complex tutorial I have seperate ligand
> and
> > protein from pdb file.
> >
> > My protein contain some missing residues so I have homology modeled the
> > protein taking the same pdb file as target and templet.
> >
> > At the time of Building the complex step I am using the homology modelled
> > protein.
> >
> > Can I add the ligand in that file as shown in tutorial:
> >
> >   163ASN      C 1691   0.621  -0.740  -0.126
> >   163ASN     O1 1692   0.624  -0.616  -0.140
> >   163ASN     O2 1693   0.683  -0.703  -0.011
> >     1JZ4  C4       1   2.429  -2.412  -0.007
> >     1JZ4  C14      2   2.392  -2.470  -0.139
> >     1JZ4  C13      3   2.246  -2.441  -0.181
> >     1JZ4  C12      4   2.229  -2.519  -0.308
> >     1JZ4  C11      5   2.169  -2.646  -0.295
> >
> > because due to homology modeling it might be possible that the
> coordinates
> > of the protein will get change??
> >
> > Or I should use maxwarn option to avoid the error message of missing
> > residues of protein pdb file and no need of homology modelling??
> >
> > Please Help
> > --
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