[gmx-users] Green fluorescent protein's chromophore

[James Starlight]

Justin,


thanks again for explanation. I'll try find other possible more
automatic ways for conversion of the itp to rtps. If I've success I'll
post here :)


James

tin Lemkul <jalemkul at vt.edu>:
>
>
> 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
>
> ========================================
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