[gmx-users] custom position restraints

[Irem Altan]

Hi,

I am trying to override the default position restraints files gromacs creates. However I get the following error during grompp:

Fatal error:
[ file posre.itp, line 5 ]:
Atom index (5) in position_restraints out of bounds (1-2).
This probably means that you have inserted topology section "position_restraints"
in a part belonging to a different molecule than you intended to.
In that case move the "position_restraints" section to the right molecule.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

When I do pdb2gmx, it creates the following .itp files:

posre_Other_chain_C4.itp    topol_Other_chain_A3.itp    topol_Protein_chain_A.itp
posre_Protein_chain_A2.itp  topol_Other_chain_A4.itp    topol_Protein_chain_B2.itp
posre_Other_chain_A3.itp  posre_Protein_chain_A.itp   topol_Other_chain_B3.itp    topol_Protein_chain_B.itp
posre_Other_chain_A4.itp  posre_Protein_chain_B2.itp  topol_Other_chain_B4.itp    topol_Protein_chain_C2.itp
posre_Other_chain_B3.itp  posre_Protein_chain_B.itp   topol_Other_chain_C3.itp    topol_Protein_chain_C.itp
posre_Other_chain_B4.itp  posre_Protein_chain_C2.itp  topol_Other_chain_C4.itp
posre_Other_chain_C3.itp  posre_Protein_chain_C.itp   topol_Protein_chain_A2.itp

with the corresponding topol files.

I created two more position restraint files to do the following:
 - restrain Calphas with force = 10K —> posre.itp
 - restrain all other protein heavy atoms (namely Protein-H & ! C-alpha) with force = 1K —> posre2.itp


I then modify topol.top as follows:

; Include forcefield parameters
#include "./amber99sb.ff/forcefield.itp"

; Include chain topologies
#include "topol_Protein_chain_A.itp"
#include "topol_Protein_chain_A2.itp"
#include "topol_Other_chain_A3.itp"
#include "topol_Other_chain_A4.itp"
#include "topol_Protein_chain_B.itp"
#include "topol_Protein_chain_B2.itp"
#include "topol_Other_chain_B3.itp"
#include "topol_Other_chain_B4.itp"
#include "topol_Protein_chain_C.itp"
#include "topol_Protein_chain_C2.itp"
#include "topol_Other_chain_C3.itp"
#include "topol_Other_chain_C4.itp"

#ifdef MAIN_POSRES
#include "./posre.itp"
#include "./posre2.itp"
#endif

; Include water topology
#include "./amber99sb.ff/tip4pew.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 "./amber99sb.ff/ions.itp"

[ system ]
; Name
Protein in water

[ molecules ]
; Compound        #mols
Protein_chain_A     1
Protein_chain_A2     1
Other_chain_A3      1
Other_chain_A4      1
Protein_chain_B     1
Protein_chain_B2     1
Other_chain_B3      1
Other_chain_B4      1
Protein_chain_C     1
Protein_chain_C2     1
Other_chain_C3      1
Other_chain_C4      1
SOL         3788
NA               6
CL               18

What could be the problem?

Best,
Irem