hi I was trying to run pdb2gmx command for gramicidin and noticed it has some D-amino acids. Reading the earlier mail wjich states that: It's not too difficult to add a new residue to the topology database. Have a look in the file ff.rtp, where is the force field you are using.
You can probably copy most parts from a standard amino acid that is similar to your new one. There are three parts for each residue: [atoms] This section maps names found in the pdb file (col 1) to atom types (col 2), charge (col 3) and charge groups (col 4). Try to have neutral charge groups. [bonds] Just define the connectivity in the residue. Names prepended with a dash ("-") refer to atoms in the next residue, if present. [impropers] Define the improper dihedrals needed to maintain chirality of the molecule. That's it - everything else like angles, normal dihedrals, and the actual parameters will be generated by pdb2gmx. I generated .itp from prodrg server and included the above stated things in .rtp file. But again when i ran pdb2gmx i got the same error.. Residue 'DLE' not found in residue topology database. What should i do? if anyone has topology file for gramicidin please send me Thanks in advance _________________________________________________________________ Call friends with PC-to-PC calling -- FREE http://get.live.com/messenger/overview_______________________________________________ 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php