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:
http://code.google.com/p/acpypi/wiki/TutorialAcpypi4Gromacs 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. Cheers, Alan > > 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. >>http://www.bio.cam.ac.uk/~awd28<<
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