On 5/29/12 6:52 AM, Steven Neumann wrote:
Ok. My topology:
; Include forcefield parameters
#include "./charmm27.ff/forcefield.itp"
; Include ligand topology
#include "ligand1.itp"
; Include Position restraint file
#ifdef POSRES_1
#include "posre_ligand1.itp"
#endif
; Include ligand topology
#include "ligand2.itp"
; Include Position restraint file
#ifdef POSRES_2
#include "posre_ligand2.itp"
#endif
; Include ligand topology
#include "ligand3.itp"
; Include Position restraint file
#ifdef POSRES_3
#include "posre_ligand3.itp"
#endif
; Include ligand topology
#include "ligand4.itp"
; Include Position restraint file
#ifdef POSRES_4
#include "posre_ligand4.itp"
#endif
; Include ligand topology
#include "ligand5.itp"
; Include Position restraint file
#ifdef POSRES_5
#include "posre_ligand5.itp"
#endif
; Include ligand topology
#include "ligand6.itp"
; Include Position restraint file
#ifdef POSRES_6
#include "posre_ligand6.itp"
#endif
; Include water topology
#include "./charmm27mod.ff/tip3p.itp"
#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif
; Include topology for ions
#include "./charmm27.ff/ions.itp"
[ system ]
; Name
Protein in water
[ molecules ]
; Compound #mols
ligand1 1
ligand2 1
ligand3 1
ligand4 1
ligand5 1
ligand6 1
SOL 4617
Each ligand.itp has [moleculetype ] - ligand1...ligand6, all other information
is the same
posre_ligand1.itp - ... - posre_ligand2.itp are all the same files.
Then when I grompp:
Syntax error - File ligand2.itp, line 7
Last line read:
'[ atomtypes ] '
Invalid order for directive atomtypes
Any suggestions appreciated,
Once you declare a [moleculetype], the other force field-level directives cannot
be called. If all the ligand topologies are the same, remove [atomtypes] from
all but the first.
-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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