Dear users, I was analysing the hydrogen bonding interaction of proteins and water in a simulation and was trying to extract specific water that forms hbond using matrix and index files generated by g_hbond.
But I found that the index file created using g_hbond has continuous water labels byt the pdb file of the system from the same trajectory does not have continuous labeling, eg, max atom number of water(SOL) is 99999 and then it restarts from 0, similarly maximum residue label of water (SOL) is 9999, then it restarts from 0. So if I want to use the number (of SOL) in index file generated from hbond to extract respective atom in pdb file will be wrong. Kindly suggest me a way out of this. Thank you Regards Kavya -- 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 [email protected].
