[gmx-users] Interactive GLU selection and dihedrals

Ivano Eberini Ivano.Eberini at unimi.it
Tue May 21 11:28:32 CEST 2002

Martedì, maggio 21, 2002, alle 05:47 , David van der Spoel ha scritto:

> Are you using the right tpr and index files for the analysis?
> You will need to make separate index files from each tpr.

Dear David,
I started from a pdb file and, using 'pdb2gmx -glu', I obtained *.top 
and *.gro with the protonated GLUH residue.
I used these two files to run MD simulation, without manually adding any 
dihedrals related to the new proton. When I run grompp, before starting 
mdrun, I got a warning about omitted dihedrals related to the (HE2) 
added proton, even if the simulation came to the end. The output 
consisted in  *.tpr and *.trr files and I tryed to analyze them:
but 'g_dih -f *.trr -s *.tpr' exited with the error message: 'Dihedral 
around 1402, 1414 not found in topology'.

I have two concerns about this problem: must I define dihedrals related 
to the added proton before running MD or it is not mandatory? If yes, 
how can I add them? Have I got to edit manually the starting *.top file?

Many thanks,
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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