[gmx-users] CHARMMff using GROMACS 4.5.3

[Justin A. Lemkul]

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

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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