[gmx-users] error in grompp

Sun Jul 8 12:02:12 CEST 2012

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?

Thank you for your help!!
Eva

>
>
> On 7/7/12 8:20 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
>> Hi everybody,
>> I want do to an energy minimization and simulation with position
>> restraints.
>> Additionally to the protein I have a membrane around my protein which I
>> also ant to fix. If I won't fix it, it is in the whole box after the
>> minimization and simulation but not around my protein.
>> Since I only want the hydrogen atoms to be flexible I use the second
>> option "protein-h" when I was asked by genrestr. This makes that the
>> whole
>> protein including the membrane of dummy atoms is fix.
>> But when I want to use grompp I get the error:
>>
>> Atom index (4942) in position_restraints out of bounds (1-4941).
>> 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.
>>
>>
>> The first 4941 atoms are of the "real" protein without the membrane and
>> after this the membrane starts:
>>
>>   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
>>    315DUM    DUM 4943   1.996   2.371   6.271
>>    316DUM    DUM 4944   1.996   2.471   6.171
>>
>>
>> When I remove the restriction of the DUM atoms I don't get the error but
>> that is not what I want.
>>
>> Can you please tell me how I can fix the membrane?
>>
>
> You need a separate position restraint .itp file.  As the error message
> states,
> position restraints are only applicable per [moleculetype].
>
> 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
>
> ========================================
>
>
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