[gmx-users] residue

Xavier Periole x.periole at chem.rug.nl
Fri Jun 11 14:47:36 CEST 2004

Dinesh Pinisetty wrote:

>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 don't know about glycerol but there an .itp file specific for
methanol. Should be in
the top directory.

>        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
>        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
When your protein is not a "classic one", meaning with regular residues,
you either
are lucky and someone has already work with special residue or you have
to build the
topology. Neither Gromacs or any program is a press botton software and
you should
be able to understand and so create your own topology ...

Good luck


   Xavier Periole - Ph.D.

   Dept. of Biophysical Chemistry / MD Group
   Univ. of Groningen
   9747 AG Groningen
   The Netherlands

   Tel: +31-503634329
   Fax: +31-503634800
   email: x.periole at chem.rug.nl
   web-page: http://md.chem.rug.nl/~periole


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