[gmx-users] Position Restraints of one of the moleculetpye

[Steven Neumann]

Ok. My topology:

; Include forcefield parameters
#include "./charmm27.ff/forcefield.itp"

; Include ligand topology
#include "ligand1.itp"

; Include Position restraint file
#ifdef POSRES_1
#include "posre_ligand1.itp"
#endif

; Include ligand topology
#include "ligand2.itp"

; Include Position restraint file
#ifdef POSRES_2
#include "posre_ligand2.itp"
#endif

; Include ligand topology
#include "ligand3.itp"

; Include Position restraint file
#ifdef POSRES_3
#include "posre_ligand3.itp"
#endif

; Include ligand topology
#include "ligand4.itp"

; Include Position restraint file
#ifdef POSRES_4
#include "posre_ligand4.itp"
#endif


; Include ligand topology
#include "ligand5.itp"

; Include Position restraint file
#ifdef POSRES_5
#include "posre_ligand5.itp"
#endif

; Include ligand topology
#include "ligand6.itp"

; Include Position restraint file
#ifdef POSRES_6
#include "posre_ligand6.itp"
#endif

; Include water topology
#include "./charmm27mod.ff/tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

; Include topology for ions
#include "./charmm27.ff/ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound        #mols
ligand1               1
ligand2               1
ligand3               1
ligand4               1
ligand5               1
ligand6               1
SOL              4617


Each ligand.itp has [moleculetype ] - ligand1...ligand6, all other
information is the same

posre_ligand1.itp - ... - posre_ligand2.itp are all the same files.

Then when I grompp:

Syntax error - File ligand2.itp, line 7
Last line read:
'[ atomtypes ] '
Invalid order for directive atomtypes

Any suggestions appreciated,

Steven




On Mon, May 28, 2012 at 5:25 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/28/12 10:48 AM, Steven Neumann wrote:
>
>> Dear Gmx Users,
>>
>> I am fighting with the position restraints. My system cosnsists of 6
>> ligands -
>> all of them have the same topology - ligand.itp. I want to:
>>
>> 1. Run NPT restraining all of ligands (easy: -DPOSRES_L, ifdef POSRE_L,
>> posre
>> ligand1.itp
>> 2. Restrain 5 of them and pull one of them away.
>>
>> Here I came across some difficulties.
>>
>> I used genrestr -f 6ligands.gro -n index.ndx -o posre1.itp
>>
>> and by index files I create an index of the ligands I wan to restrain.
>> Each my
>> ligands has 46 atoms. When I process to grompp:
>>
>> Atom index (256) in position_restraints out of bounds (1-46).
>> This probably means that you have inserted topology section
>> "position_restraints
>>
>> Shall I rename Ligands as different residue names? If my posre includes
>> 1-46
>> atom all ligands are restraints? How to restrain just 5 out of 6 of them?
>>
>>
> Position restraints are applied on a per-moleculetype basis.  If you have
> six copies of a ligand, the only way to do this is to define the sixth as a
> special [moleculetype] (even if it contains identical information) with a
> different name, such that it can be restrained in the absence of restraints
> on the others.  See the logic here:
>
> http://www.gromacs.org/**Documentation/Errors#Atom_**index_n_in_position_*
> *restraints_out_of_bounds<http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds>
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
> --
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