[gmx-users] error in grompp

[Justin A. Lemkul]

On 7/8/12 6:02 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> Hi Justin,
> thank you for your answer.
>
> Now I tried it with two different restraint .itp files. One for the
> protein and one for the dummy atoms.
> But still it doesn't work. Now the error is:
>
> [ file posre_memb.itp, line 5 ]:
> Atom index (4942) in position_restraints out of bounds (1-1).
> 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.
>
>
> But I think I included it the right way:
>
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Include water topology
> #include "amber03.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 "amber03.ff/ions.itp"
>
> #include "amber03.ff/dum.itp"
> #ifdef POSRES
> #include "posre_memb.itp"
> #endif
>
>
>
> In my coordiate file the difference between them look like this:
>
> 313LEU   HD23 4938   3.813   4.505   3.308
>    313LEU      C 4939   3.435   4.335   3.190
>    313LEU    OC1 4940   3.429   4.330   3.090
>    313LEU    OC2 4941   3.337   4.305   3.259
>    314DUM    DUM 4942   1.996   2.371   6.171
>    314DUM    DUM 4943   1.996   2.371   6.271
>    314DUM    DUM 4944   1.996   2.471   6.171
>    314DUM    DUM 4945   1.996   2.471   6.271
>
>
> my restraint file for the protein looks like this:
>
>
> ; position restraints for Protein-H of GROup of MAchos and Cynical Suckers
>
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>     1    1       1000       1000       1000
>     4    1       1000       1000       1000
>     7    1       1000       1000       1000
>    10    1       1000       1000       1000
>    13    1       1000       1000       1000
>
>
> and my restraint file for the dummy atoms look like this:
>
> ; position restraints for Protein-H of GROup of MAchos and Cynical Suckers
>
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
> 4942    1       1000       1000       1000
> 4943    1       1000       1000       1000
> 4944    1       1000       1000       1000
> 4945    1       1000       1000       1000
>
>
> What is wrong?
>

Atom numbering is done per [moleculetype] and has nothing to do with the atom 
numbers in the coordinate file.  If you have a one-atom dummy [moleculetype], 
then the only valid content of posre_memb.itp is:

[ position_restraints ]
;  i funct       fcx        fcy        fcz
    1    1       1000       1000       1000

-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

========================================