[gmx-users] residue

[Dinesh Pinisetty]

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 searched in the .rtp of all the force fields I could not find the
residue which is present in the pdb file.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.
Thanks in advance.....................
Thanking you,
Yours sincerely,
Dinesh pinisetty