[gmx-users] Interactive GLU selection and dihedrals
Ivano.Eberini at unimi.it
Tue May 21 09:50:57 CEST 2002
Dear GROMACS users,
I am trying to run two different protein MD simulations starting from
the same crystallographic data: I'd like to make a comparison between
the protein with all unprotonated glutamic acid residues (GLU) and the
same structure with just one more proton on a glutamic acid residue
(GLUH). I used pdb2gmx with the option -glu (interactive glutamic acid
selection) to protonate the target residue.
MD started with a warning about dihedrals; after the end of MD
calculation, g_dih applied on the trajectory file exited with the
"Dihedral around 1402, 1414 not found in topology"
Is there a tool to define the lacking dihedrals? Have I got to discard
this trajectory file and re-run MD simulation after they are fixed?
Thanks in advance and best regards,
Gruppo di Studio per la Proteomica e la Struttura delle Proteine
Dipartimento di Scienze Farmacologiche
Università degli Studi di Milano
Via G. Balzaretti, 9
20133 - Milano
Tel.: +390250318359-8304/-8359 Fax: +390250318284
SPIRITVS DVRISSIMA COQVIT
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