[gmx-users] Missing Residues of PDB file

[rama david]

Dear Neha,
    It is right as per my opinion. if the end residue is missing no issue.
join the ligand pdb and receptor pdb and use pdb2gmx directly .
 no need to do as per total process of Justin tutorial. As justin tutorial
is
for the non-amino acid residues.
    use properly the pdb2gmx command and see the output on screen carefully.

 With Best regards,
Rama david



On Mon, Aug 25, 2014 at 3:49 PM, neha bharti <nehabharty123 at gmail.com>
wrote:

> 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
> --
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