[gmx-users] Green fluorescent protein's chromophore

[James Starlight]

Hi Bharat,

That simulation have been done in charmm program so the convertion
from charmm to gromacs would be more routinely for me.


James

2012/12/5 bharat gupta <bharat.85.monu at gmail.com>:
> Hi,
>
> You can refer this paper for the topology
> http://pubs.acs.org/doi/abs/10.1021/jp014476w.
>
> -----------
> BHARAT
>
> On Wed, Dec 5, 2012 at 10:14 PM, James Starlight <jmsstarlight at gmail.com>wrote:
>
>> Dear Gromacs Users!
>>
>>
>> I'm looking for the model as well as for the pre-paired topology for
>> any kind of GFP protein with the chromophore group covaletnly bonded
>> in the interiour of that protein.
>>
>> Some times ago I've tried to make such models by hands but I've forced
>> with some difficulties with the integration of the chromophore group
>> to the existing GROMOS force field parameter files. In that case I had
>> .itp for the chromophore group made by PRODRG which I've failed to
>> convert to the rtp and integrate to other files in accordance to the
>>
>> http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field
>>
>> So I'll be very thankfull if any could provide me with such model as
>> well as suitable topology which I could use as the example for
>> preparation of my future models :)
>>
>>
>> Thanks for help
>>
>> James
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