[gmx-users] residue

David spoel at xray.bmc.uu.se
Fri Jun 11 00:08:56 CEST 2004

On Thu, 2004-06-10 at 21:58, 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 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.

check other topologies in gmx/share/top and modify as necessary. Check
chapter 5 of the manual.

> Thanks in advance.....................
> Thanking you,
> Yours sincerely,
> Dinesh pinisetty
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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