Anna Marabotti wrote:
Dear all,
I would like to do a position restraint MD by applying position
restraints not only to my protein but also to its ligand. In order to do
it, I created with genrestr a new protligposre.itp file in which I
indicated the group to be restrained as Protein_lig. In this
protligposre.itp file, therefore, there are restraints on the protein
and on the ligand together.
Then, I modified the .top file in order to include the statement for the
position restraints. I tried to modify first the usual statement:
#ifdef POSRES
#include 'posre.itp'
#endif
to
#ifdef POSRES_PROTLIG
#include 'protligposre.itp'
#endif
(obviously, in my .mdp file I have the statement define = -DPOSRES_PROTLIG)
Since it did not work, I used:
#ifdef POSRES
#include "protligposre.itp"
#endif
(obviously, the statement in the .mdp file was modified to -DPOSRES)
Then, I tried to ADD (not to replace) a new
#ifdef POSRES_PROTLIG
#include "protligposre.itp"
#endif
and I tried all the positions in the .top file.
Every time, I obtained an error stating:
Fatal error:
[file protligposre.itp, line 2822 (this number changes every time I
change the position of the statement in the .top file)
Atom index (2818) in position_restraints out of bounds (1-2817).
This probably means that you have inserted topology section
"position_restraints" in a part belonging to a different molecule that
you intended to. In that case, move the "position_restraints" section to
the right molecule.
I really don't know what is the correct position for this statement,
since I tried all position that I could, starting just below the already
present statement!
Moreover, another doubt I have is: is it correct to include protein and
ligand in the same posre.itp file? In case it is not correct, what is
the correct position in the .top file to insert the ligposre.itp file
(the file containing position restraints for ligand only)? Please
consider that in my .top file the topology of the ligand was added with
the statement
#include "lig.itp"
just below the statement for the forcefield.
Position restraints are applied on a per-moleculetype basis, hence why you're
getting an "out of bounds" error - the posre.itp file specifies more atoms than
are in your "Protein" moleculetype. There are two possible solutions:
1. Merge the moleculetypes of Protein and Ligand (i.e., re-write the topology -
yuck)
2. Make a separate posre.itp file for the ligand only.
There is an example of #2 on the Gromacs site (most errors are described and
solved there):
http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds
-Justin
Thank you very much
Anna
__________________________________________________________________
Anna Marabotti, Ph.D.
Laboratory of Bioinformatics and Computational Biology
Institute of Food Science - CNR
Via Roma, 64
83100 Avellino
Phone: +39 0825 299651
Fax: +39 0825 781585
E-mail: [email protected] <mailto:[email protected]>
Skype account: annam1972
Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm
"When a man with a gun meets a man with a pen, the man with the gun is a
dead man"
--
========================================
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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