[gmx-users] Regarding ffG43a1p force field

[Ramachandran G]

Hi,
   That is the problem. Yet i do not know whether it is working fine
not.....i have been working with that for nearly 9-10months but not
satisfied yet.
In the following mail i will cut and paste the force field parameters which
you can use it with amber. If you have time please go ahead and modify
according to your wish.

Regards,
Rama


On Wed, Jun 22, 2011 at 11:27 PM, bharat gupta <bharat.85.monu at gmail.com>wrote:

> Dear Sir,
>
> It will be of great help to send the force field. actually I want to know
> whether it was working fine for u or not ?? ... Pls send the file and if
> it's working fine then I think you can deposit it in User contributions in
> gromacs repository...
>
>
> On Thu, Jun 23, 2011 at 2:38 PM, Ramachandran G <gtrama at gmail.com> wrote:
>
>> 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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>>>>
>>>> --
>>>> Postdoctoral Research Scholar,
>>>> Department of Chemistry,
>>>> 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
>>> E-mail : monu46010 at yahoo.com
>>>
>>>
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>>
>>
>>
>> --
>> Postdoctoral Research Scholar,
>> Department of Chemistry,
>> 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
> E-mail : monu46010 at yahoo.com
>
>
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-- 
Postdoctoral Research Scholar,
Department of Chemistry,
University of Nevada, Reno.
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