Hello, I am trying to run the following command but I always get error I download my PDB from https://www.rcsb.org/structure/2J3S Then I remove water, ligand and keep only chain A by pymol Then I mutate the site that I am interested in and you can find the new PDB here https://www.dropbox.com/sh/4r9jhrwmgfmodh6/AAB8TJYep7NvO7w7APJY0PlAa?dl=0
then I run the following gmx pdb2gmx -f A2236.pdb -o conf.pdb No matter which force field I use, I get an error like Fatal error: Residue 271 named SER of a molecule in the input file was mapped to an entry in the topology database, but the atom CA used in that entry is not found in the input file. Perhaps your atom and/or residue naming needs to be fixed. can anyone help me to fix the problem? Many thanks Mohammad -- 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].
