[gmx-users] Green fluorescent protein's chromophore

[Justin Lemkul]

On 12/5/12 11:19 AM, James Starlight wrote:
> Justin,
>
> 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
> routinely.
>

I don't know of a way to convert .itp files into .rtp entries, though it could 
probably be done.  The time investment in developing such a script may not be 
worth it, since creating an .rtp entry is rather simple following the guide in 
the manual and existing entries (i.e. amino acids).  The choice (script vs. 
manual effort in a text editor) is up to you.  I've done similar things with 
other people before, so it's certainly possible, though a bit tedious, 
especially for the GFP chromophore since there are lots of atoms involved.  I 
worked with it several years ago and I simply did it by hand using the 
parameters that were suggested to you earlier for CHARMM.

-Justin

>
> James
>
> 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
>>
>> ========================================
>>
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> * Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

-- 
========================================

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

========================================