[gmx-users] GFP chromophore topology help

Justin A. Lemkul jalemkul at vt.edu
Wed Nov 10 00:22:42 CET 2010

Ramachandran G wrote:
> Dear gromacs users:
>         I have constructed the Amber03 force fields parameters
> (bonds,angles, proper and imporer dihedral.....) for the chromophore
> (p-hydroxybenzylidene-imidazolinone) inside GFP system and got the
> topology. But after energy minimization of the system, the
> conformation of the chromophore totally changed and the benzene and
> imidazole ring got puckered although i did not got any error message.

No Gromacs tool will check your work for you.  It will do what you tell it. 
Likely you omitted some necessary bonded parameters (bonds, angles, impropers, 
etc).  Either that, or the parameters you supplied produce the incorrect behavior.


> Could anyone help me? Thank you.
> with regards,
> Rama


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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