[gmx-users] Missing Residues of PDB file

[RINU KHATTRI]

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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