[gmx-users] question about dihedral angles check,reload

Adriana Pietropaolo adriana at ms.fci.unibo.it
Mon Feb 20 09:25:12 CET 2006

  Hi gmx users,
I repost the same question, because I've not a reply...
  I've a doubt about the dihedral angles written in the file .top 
generated by pdb2gmx.
  When I try to run g_rama, there was a fatal error because in the 
topology file lacked some dihedrals, but I check the topology file and in 
  the dihedrals part the four atom numbers are written for each 
  torsions of my protein, followed by 3. 
  However the chi dihedrals label as HIS_chi... are not
  consecutively written as in the protein sequence.
Furthermore if I run editconf -f (the tpr file) the output is correctly 
The error is only in the torsion, but to calculate a dihedral is not 
sufficient the atom coordinates?
But I'm very afraid for the reading of torsion parameters...  
How can I do to verify that the torsions is good...the torsions is the 
central part of dynamics... 

Adriana Pietropaolo,
PhD student,
dipartimento di Chimica Fisica ed Inorganica,
Facolta' di Chimica Industriale
Universita' di Bologna
Tel 051/6446992
FAX 051/2093690 

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