[gmx-users] Green fluorescent protein's chromophore

[Justin Lemkul]

On 12/5/12 11:46 AM, James Starlight wrote:
> Justin,
>
>
> So as I understood such problems might be with all proteins consisted
> of prostetic groups ( Rhodopsin, myoglobin etc). Is there more trivial
> way to obtain parametrized models of such proteins with gromacs force
> fields if I have itp's of the prostetic groups made by external
> software ?
>

In general, a prosthetic group that is not bound covalently is handled by .itp 
files, anything covalently attached is handled by .rtp entries.  If you have an 
.itp file for a covalently bound compound, then you need to convert it to .rtp 
using the contents of the .itp.  After all, everything we're talking about is 
topological information, just in different formats.

-Justin

>
> Thanks for help
>
> James
>
> 2012/12/5 Justin Lemkul <jalemkul at vt.edu>:
>>
>>
>> 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
>>>>
>>>> ========================================
>>>>
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>>
>>
>> --
>> ========================================
>>
>> 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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-- 
========================================

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

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