[gmx-users] Missing Residues of PDB file

neha bharti nehabharty123 at gmail.com
Mon Aug 25 07:24:42 CEST 2014

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

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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