Hello, I am experimenting with formatting pdb files using pdb2gmx. Currently I am downloading ligand files from RCSB.ORG. These are non-protein pdb files. When I look at their residues, instead of having a standard residue, they use their pdb id as the residue id. pdb2gmx does not like this because these are not standard residues. Is there a setting I can use to make pdb2gmx to ignore this? Otherwise I can use a sed command to replace all instances of a given residue name. However, when I try replacing with a standard residue name, I still run into errors.
Here is an example ligand pdb file http://www.rcsb.org/pdb/files/ligand/002_ideal.pdb Notice instead of having a standard residue it uses 002 ATOM 1 C1 002 A 1 -1.036 0.293 0.447 1.00 10.00 C ATOM 2 C2 002 A 1 -1.041 1.804 0.685 1.00 10.00 C ATOM 3 C3 002 A 1 -2.288 2.191 1.482 1.00 10.00 C .... Any advice? Does GROMACS only support the standard 20 amino acids? -- Jack _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
