[gmx-users] PRODRUG itp-file is not understood by grompp

Anastassia Alexandrova anastassia.alexandrova at yale.edu
Mon Apr 2 14:55:05 CEST 2007

Hello All!
I am trying to run GROMACS for a protein containing a ligand. I use the PRODRUG
machinery to prepare .itp file for the ligand, following all the instructions in
the Kerrigan's Manual. I have introduced one change in the produced .itp file
for the ligand: I changed the atom types produced by PRODRUG to the
corresponding OPLS-AA atom types. Also, in the .top file for the protain, I
included a statement: #include "ffoplsaa.itp"
However, when I start energy minimization, grompp complains that it cannot find
atom type CA (the first atom in my ligand). CA is an existing OPLS-AA type.
What am I doing wrong? Is there anything else that I must modify before using
OPLS-AA atom types?
Thank you much!
     Anastassia Alexandrova, Ph.D.
           Yale University
       Department of Chemistry
         225 Prospect Street
       New Haven, CT 06520-8107
         Phone: 203-432-6288
          Fax: 203-432-6144
    anastassia.alexandrova at yale.edu

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