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. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.