[gmx-users] A quick question regarding topology generation

Agnivo Gosai agnivogromacs14 at gmail.com
Fri Feb 6 21:38:01 CET 2015

Dear Users

During topology generation many a times we clean the PDB file by stripping
it off waters ( crystallized ) or some other small molecules ( like a small
ligand ) etc , which are of no immediate interest , as we concentrate on
getting the structure for the protein ( biomolecule ) upon which we want to
perform molecular dynamics.

My question is will that create any distortion on the protein structure
generated by "pdb2gmx"? One of my colleagues told me that the other atoms
like those of the water and the small ligands may be participating in
hydrogen bonds with the protein which can stabilize the structure. So if I
remove them then I am making the protein structure unstable. I told him
that I do energy minimization after solvation to stabilize my structure but
he is saying that it is unstable since the beginning.

I know that I can use RMSD , DSSP to validate the structure but still I am
not able to figure out an answer to his question.

Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.

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