On 9/18/12 12:42 PM, SIMONE BROGI wrote:
Dear gromacs user,
I have a complex generated by docking calculation and I would perform a MD
by gromacs. I have a problem with ligand atoms. In the pdb file the ligand
appears as UNK and if I process this file in order to start simulation I
receive this messagge error:
"Residue 'UNK' not found in residue topology database"
this part of file concerning ligand and it is not a residue. In order to
fix this problem can I replace the UNK with another tag that is Known in
topology database for a ligand??? or How can I fix this error???
Most ligands are not part of existing force fields. Please consult the
following:
http://www.gromacs.org/Documentation/Errors#Residue_'XXX'_not_found_in_residue_topology_database
http://www.gromacs.org/Documentation/How-tos/Parameterization
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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