[gmx-users] CHARMMff using GROMACS 4.5.3

Justin A. Lemkul jalemkul at vt.edu
Thu Nov 24 01:02:32 CET 2011

Gideon Lapidoth wrote:
> Hi all,
> I am trying to run a simulation of a protein and ligand system using 
> Gromacs 4.5.3 and CHARMMff. prior to running this system I ran the 
> protein as is with out adding the ligand, and the simulation was fine.
> Ligand parametrization was done using the SwissParam server. when trying 
> to run EM I got the following error message:
> "Syntax error - File ligand.itp, line 7
> Last line read:
> '[ atomtypes ] '
> Invalid order for directive atomtypes"
> Obviously the outputted itp format given by SwissParam is wrong. can 
> anyone direct me as to the changes needed to correct this mistake?

The .itp file is probably correct but your manner of adding it to your .top is 
wrong.  The topology hierarchy must be observed, so if a new molecule needs new 
[atomtypes], then they must be #included prior to the declaration of *any* 
[moleculetype].  Likely your #include statement is simply misplaced, and should 
be something like:

#include "charmm27.ff/forcefield.itp"

#include "ligand.itp"

(remaining protein-related stuff)



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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