[gmx-users] custom position restraints

[Mark Abraham]

Hi,

As the warning (and docs) say, position restraint interactions are
generated, like other interactions, per molecule(type). You are presumably
trying to get them to act on the whole system, which can't be done this way.

Mark

On Fri, 22 Jul 2016 20:26 Irem Altan <irem.altan at duke.edu> wrote:

> 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
>
> --
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