[gmx-users] Interactive GLU selection and dihedrals

David van der Spoel spoel at xray.bmc.uu.se
Tue May 21 19:40:37 CEST 2002

On Tue, 21 May 2002, Ivano Eberini wrote:

>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'.
This message indicate (after checking the source code...) that you have a 
dihedral angle defined without force field parameters. grompp gives a 
warning about that. This probably is the one defining the CD-OE2 bond.
You didn't say which force field, but you need to use:
180 69.87 2
according to the GROMOS96 ff. (see dihedral gd_3 in  ffG43a1bon.itp).

If you add this to your topology file and rerun grompp, you can do your 
analysis again. It is probably not necessary to redo the simulation. Since 
your GLUH is probably hydrogen bonded it will not start spinning like mad.

>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?

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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