[gmx-users] pdb2gmx error "residue not found in residue topology database"
peter.stern at weizmann.ac.il
Wed Jul 8 19:51:42 CEST 2015
Look at the file: residuetypes.dat in the ../top/ directory of your installation.
It lists all the residue names and more.
Sent from my iPad
> On 8 ביולי 2015, at 17:45, Hamisu Aliyu Mohd <hamisu.kazaure at yahoo.com> wrote:
> Dear gmx-users,
> I am really new in this field of endeavour and I am trying investigate the solubility of peptides in organic solvents, I built a simple tripeptide (gly-gly-gly) using Gaussian 5.0 and I convert the output file(.out) to .pdb. I am now trying to use pdb2gmx tool to generate topology for my peptide using GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) I was promoted with an error "residue not found in residue topology database” I checked GROMACS website at http://www.gromacs.org/Documentation/Errors I learned the residue must have the same name as in the force field, please I don’t know the naming convention of this force field please HELP.
> Ali H.
> Department of Chemistry
> University Dutse
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