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
--
========================================
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
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
