[gmx-users] residues

Dinesh Pinisetty dpinis1 at lsu.edu
Thu Jun 10 21:14:01 CEST 2004

Hi all,
        Is there anyway to avoid the problem because of residues.When I
imported a pdb file for Glycerol or methanol etc I am getting an error as
--- residue is not present in the residue topology database.
        I am using G43a1 force field so I went to ffG43a1.rtp and searched
for that particular residue but i could not find it there,I serached .rtp
entries of all the other forcefields I could not find the residue.
        So,I thought probably it was mentioned as other name in the .rtp
entry and taken a list of all the atoms for that missing residue from the
pdb file and searched for a list of all those atoms in the .rtp entry still
I could not find the atoms,some atoms were not seen in the whole .rtp
entries.it took me many hours to do all these.
        Now,is it possible to run Md simulation with this pdb file using
Gromacs as it is not creating topology and gromacs files I do not think it
is possible.Its going to be problem not only to me but all others if there
is no conjunction between pdb files and .rtp entries in GROMACS.
How to solve this problem if anyone can answer these questions I will be
very grateful to you.I am just a beginner and I want learn this from
basics,as of now everyday i will be getting some or the other error when i
try to import pdb files and try to run the simulation.
Thanks in advance.....................
Thanking you,
Yours sincerely,
Dinesh pinisetty.

More information about the gromacs.org_gmx-users mailing list