[gmx-users] Missing Residues of PDB file (rama david)
nehabharty123 at gmail.com
Mon Aug 25 12:16:59 CEST 2014
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??
Thank you very much.
> 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
>you can model the protein and then align it with pymol align command or any
>other visualizing software.
>With beat regards,
On Mon, Aug 25, 2014 at 11:01 AM, RINU KHATTRI <nickname.mittu at gmail.com>
> use -missing in last of command pdb2gmx
> On Mon, Aug 25, 2014 at 10:54 AM, neha bharti <nehabharty123 at gmail.com>
> > 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
> > 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
> > 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
> > 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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