[gmx-users] Interactive GLU selection and dihedrals

David van der Spoel spoel at xray.bmc.uu.se
Tue May 21 17:47:27 CEST 2002

On Tue, 21 May 2002, Ivano Eberini wrote:

>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"

Are you using the right tpr and index files for the analysis?

You will need to make separate index files from each tpr.

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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