[gmx-users] Interactive GLU selection and dihedrals

[Ivano Eberini]

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 
following message:
"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,
Ivano
--
Ivano Eberini
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

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