[gmx-users] question about dihedral angles check,reload
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...
dipartimento di Chimica Fisica ed Inorganica,
Facolta' di Chimica Industriale
Universita' di Bologna
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