[gmx-users] Regarding ffG43a1p force field

[Ramachandran G]

Why you are doing simulation without chromophore? Chromophore is important
in GFP. If you want i can send you the forcefield which i am using for GFP.

Rama

On Wed, Jun 22, 2011 at 10:29 PM, bharat gupta <bharat.85.monu at gmail.com>wrote:

> Hi Sir,
>
> Actually I am doing the simulation without the chromophore. So, planarity
> does not matter to be ..
>
>
>
> On Thu, Jun 23, 2011 at 2:23 PM, Ramachandran G <gtrama at gmail.com> wrote:
>
>> Hi Bharat,
>>     I used Amber force field, but still i am not statisfied with the
>> parameters which i used because after some nanosecond simulation(1 -2 ns)
>> the planarity of the sturcture changes. I tired changing the force
>> constant but still not much successfull. If you got success please let me
>> know.
>>
>> with regards,
>> Rama
>>
>> On Wed, Jun 22, 2011 at 10:11 PM, bharat gupta <bharat.85.monu at gmail.com>wrote:
>>
>>> Hi,
>>>
>>> I want to simulate a docked complex of my protein (GFP) with
>>> phosphotyrosine. I have found this - ffG43a1p forcefield contains parameters
>>> for pTYR, so I want to know how good is this FF for simulating my system...
>>> As in the literature its mentioned that people have used CHARMM, AMBER, OPLS
>>> ff for simulation of GFP. So, using this will be a correct choice or not ...
>>>
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>>
>>
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>> University of Nevada, Reno.
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>
>
>
> --
> Bharat
> Ph.D. Candidate
>
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
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-- 
Postdoctoral Research Scholar,
Department of Chemistry,
University of Nevada, Reno.
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