[gmx-users] Using OPLSAA
sistla.lists at gmail.com
Fri Sep 9 05:58:14 CEST 2005
I am a rank new user of gromacs. I could use the Drug-Enzyme complex
tutorial and run the simulation given in that.
However, I am attempting to run it on protein of my choice now. Also I would
like to use the OPLS ff. I am encountering a difficulty here. When I make
the ligand .gro file using the PRODRG server at Dundee, I think the server
uses Gromacs ff. Obviously when I incorporate this ligand .top file into my
protein and use the .itp file thrown out by PRODRG, the program ends because
of conflict where it says 'ATOM type O not found' or similar. I think the
trouble is my topology file of the protein was created with opls where as
that of logand was done with gmx. How do I overcome this difficulty?
Thanks for your patient reading and any help.
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