[gmx-users] Re: ligand protein complex with ffamber99

Alan alanwilter at gmail.com
Mon Nov 24 10:13:24 CET 2008

Hello Ragnarok,
I am the author of acpypi and I believe Mark's guessing right. I strongly
suggest you to look my simple tutorial for some warnings about where to
place correctly the entries for amberff in *.top file:


In particular: "*NB(1):* #include "Ligand.itp" has to be inserted right
after ffamber**.itp line and before Protein_*.itp line in *Complex.top*."

I intendo to update this tutorial for a more realistic situation (i.e.,
using PME for instance, etc.), but only in Jan when I intend to make an
official release. I also suggest to use latest revision o acpypi since I
updated that last week.

I also want people to know that I tested acpypi and ffAMBER for GMX 3.3.1
with GROMACS 4.0.2 and seemed to work like a charm.


> Ragnarok sdf wrote:
> > I am trying to setup a simulation with a ligand and a protein using
> > ffamber99 forcefield. I have already generated the ligand's topology
> > file using acpypi and everything seems to be all right in the files
> > generated. However, while following the steps in the drug enzyme
> > tutorial provided in the gromacs' web site, after i add the ligand to my
> > protein's .gro file and edit the lines in my topology file to include
> > the ligand's topology, when i type the command editconf, my ligand
> > dissapears from my .gro file. The .gro generated from my original
> > ligand-protein complex.gro does not include my ligand coordinates
> > whatsoever.
> I'm guessing you've added your ligand to the end of the file, but not
> adjusted the total number of atoms at the top of the file.
> Mark
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
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