[gmx-users] Missing Residues of PDB file (rama david)

[neha bharti]

Hello Rama david

Thank you very much for your reply.

The residue is missing from the middle as well as from the end. Hence I
have modeled it with the help of homology modeling.
Then I align both the protein (PDB downloaded as well as homology modelled)
and get a RMSD fluctuation of 0.45 with the help of pymol.
My Method is correct or not??

Please Help
Thank you very much.

With regards
Neha bharty


>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