[gmx-users] topology error

[parinald at unsl.edu.ar]

Thans`s David and Patricia:
                           I check the topology very times carefully
but the error message is the same;

#define _FF_GROMOS96
#define _FF_GROMOS96A

  [defaults]
1    1    no    1.0    1.0
  ..........
  ..........
;new start the molecular definitions
  [moleculetype]
  [atoms]
  [bonds]
  [pairs]
  [angles]
  [dihedrals]
  [dihedrals]
#include "dmso.itp"
  [system]
Protein
  [molecules]
Protein      1
DMSO       3579

                     there is any way to look out how gromacs read the
topology file?. Somebody has worked out with convert
topology?
               Thank`s again.


> On Fri, 2004-09-17 at 00:06, parinald at unsl.edu.ar wrote:
>> Hi All:
>>        I have a non-protein molecule in DMSO.
>> After convert gromos96 topology file to Gromacs topology (with convert
>> program), I try to execute grompp...
>>
>> processing topology...
>> Generated 0 of the 946 non-bonded parameter combinations
>> Cleaning up temporary file grompp9xctdT
>> Fatal error: Moleculetype Protein contains no atoms
> you'll have to check the .top file with chapter 5 of the manual close
> by. There definitely is an error in the topology but it's impossible to
> judge what. Maybe missing [ atoms ] section?
>>
>> I don`t know how to avoid (or solve) this problem, any idea?
>>                                               Thank you very very much.
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> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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