[gmx-users] Green fluorescent protein's chromophore

James Starlight jmsstarlight at gmail.com
Wed Dec 5 17:19:55 CET 2012


The GFP protein consist of chromophore group which matured after
folding of that protein. That prostetic group is the cyclized
derivative of the Ser-Tyr-Gly peptide which is the part of the
alpha-helix of that protein surrounded by the beta-barell interiour.

So I want to make simulation of such protein consisted of covalently
bonded prostetic group. I've made parametrisation of that isolated
chromophore but couldn't integrate it into GROMOS force field because
aminoacids.rtp didnt work with ITP file produced by PRODRG. It's also
inportant that different mutants of GFP consist of different types of
that chromophores so manual conversion of the ITP to RTP formats in
each cases ( I'd like to simulate different mutants) would be very


2012/12/5 Justin Lemkul <jalemkul at vt.edu>:
> On 12/5/12 11:00 AM, James Starlight wrote:
>> Hi Bharat,
>> That simulation have been done in charmm program so the convertion
>> from charmm to gromacs would be more routinely for me.
> I think it would be better if you describe exactly what you need help with.
> If it's a matter of having parameters in CHARMM format but not Gromacs
> format, then all you need is to follow the manual to implement the
> parameters.  If you're having a specific problem along the way, please
> describe it fully and specifically, otherwise the default response is
> "everything's in the manual and elaborated on at the webpage you already
> quoted."
> -Justin
> --
> ========================================
> Justin A. Lemkul, Ph.D.
> Research Scientist
> 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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