[gmx-users] where to insert a new include DPOSRES in topology file?
Justin A. Lemkul
jalemkul at vt.edu
Fri Feb 18 12:48:42 CET 2011
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: amarabotti at isa.cnr.it <mailto:amarabotti at isa.cnr.it>
> 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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