[gmx-users] GFP chromophore topology help

[Ramachandran G]

Thank you for the help.
       I have successfully constructed the chromphore molecule but
still have problem in connecting it to the neigbhouring residues. I
don't know how the connection sequence needs to be given in gromacs.
Please help

with regards,
Rama

On Tue, Nov 9, 2010 at 3:22 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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.
>
> -Justin
>
>> Could anyone help me? Thank you.
>>
>>
>> with regards,
>> Rama
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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-- 
Postdoctoral Research Scholar,
Department of Chemistry,
University of Nevada, Reno.