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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