[gmx-users] Green fluorescent protein's chromophore

[James Starlight]

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 ?


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
>>>
>>> ========================================
>>>
>>> --
>>> 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
>
> ========================================
> --
> 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