[gmx-users] position restraints

Xavier Periole x.periole at chem.rug.nl
Mon Apr 26 15:51:00 CEST 2004

David wrote:

>On Fri, 2004-04-23 at 22:51, Pedro Alexandre Lapido Loureiro wrote:
>>I am trying to restrain a molecule (atoms 18208 .. 18220) in my system using 
>>the file posre.itp.
>>When I run grompp, it crashes saying:
>>"Atom index (18208) out of bounds (1 - 3)"
>>Do you have any suggestions?
>seems like the include statement is after the water molecule rather than
>directly after the protein
>>Pedro Alexandre Lapido Loureiro
>>Laboratório de Física Biológica
>>Instituto de Biofísica
>>gmx-users mailing list
>>gmx-users at gromacs.org
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Remember that the numbering begins with the first atom of the protein. 
If the
solvent is before the protein you do not count it. The constraints must 
be on the
atom number of the protein topology alone.



   Xavier Periole - Ph.D.

   Dept. of Biophysical Chemistry / MD Group 
   Univ. of Groningen
   9747 AG Groningen
   The Netherlands

   Tel: +31-503634329
   Fax: +31-503634800
   email: x.periole at chem.rug.nl
   web-page: md.chem.rug.nl/~periole

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