On 8/22/13 7:13 AM, Shima Arasteh wrote:
yes, but there was only a typing mistake in my earlier email.
Always copy and paste; don't re-type.
The error I get still exists when I use the correct itp file:
First made an .itp file of the ion: ion_posre.itp
Then added these line to top file:
#include "./charmm36-modified.ff/ions.itp"
#ifdef POSRES_ION
#include "ion_posre.itp"
#endif
And added the line to mdp file
define = -DPOSRES_ION
Position restraints must be placed within the [moleculetype] to which they
correspond. Right now, you're declaring a force field and then saying you want
to restrain an ion that does not exist because it hasn't been introduced in the
topology.
http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds
-Justin
--
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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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