On 3/18/13 12:47 PM, Parshvika Sharma wrote:
Dear gromacs users,
I want to run a protein ligand MD in Gromacs 4.6 using CHARMM forcefield.
My system consists of 2 non-covalently bound ligands (FAD and NADPH) in the
active site. I generated the topology files (*.itp) of ligands using
SWISSPARAM. Before running the energy minimization, I added the *.itp file
for both ligands in topol.top file as mentioned in the gromacs tutorial.
#include "charmm27.ff/forcefield.itp"
#include "FAD.itp"
#include "NDP.itp"
But while running GROMPP I am getting this error,
Syntax error - File NDP.itp, line 7
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes
It just accepts the first *.itp mentioned in the topol.top, be it FAD.itp
or NDP.itp and shows this error for the file mentioned next.
I would like to know the correct way to mention *.itp in topol.top, if we
have more than 1 ligand.
If each .itp file introduces new [atomtypes], you can't simply #include them.
All [atomtypes] (like any force field-level directive) must be declared before
any [moleculetype] is declared. I posted a detailed explanation of this within
the last few weeks (hint: check the archive, most topics like this have been
discussed at length many times).
Net effect? Merge the two [atomtypes] directives before #including any new
[moleculetype] blocks.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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