[gmx-users] error in grompp

[reisingere at rostlab.informatik.tu-muenchen.de]

Hi Justin,
thank you very much for your help!!

>
>
> 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
>
> ========================================
>
>
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