Quoting Dariusz Plewczynski <[EMAIL PROTECTED]>:
Dear Sirs,
I have a problem with running the short simulation with GROMACS. I have
a structure for a small ligand (drg.pdb after cleaning with PRODRG). For
this ligand I have run PRODRG in order to get drg.gro file and drg.itp
topology file. I have edited the drg.top in order to include drg.itp as
#include. My goal is to run simulation in vacuum (no water) - with only
ligand (!). No protein also. I have tried to run it but I am getting
error message. It seem that GROMACS does not read my topology file. What
I am doing wrong ?
grompp -f em.mdp -c drg.gro -p drg.top -o drg.tpr
Results:
....
creating statusfile for 1 node...
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 1284 of the 1485 non-bonded parameter combinations
processing coordinates...
Fatal error: number of coordinates in coordinate file (drg.gro, 25)
does not match topology (drg.top, 0)
You need to input the itp file generated by PRODRG of your drug into
your drg.top file.
do that by #include "/your filepathway/drg.itp"
Regards
Dariusz
--
Farid Sa'adedin
Membrane Biophysics Laboratory
Department of Veterinary Biomedical Sciences
College of Medicine & Veterinary Medicine
Royal (Dick) School of Veterinary Studies
University of Edinburgh
Summerhall
Edinburgh EH9 1QH
SCOTLAND
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