[gmx-users] Regarding ffG43a1p force field

[bharat gupta]

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 ...
>>>>
>>>> --
>>>> Room No. : 7202A, 2nd Floor
>>>> Biomolecular Engineering Laboratory
>>>> Division of Chemical Engineering and Polymer Science
>>>> Pusan National University
>>>> Busan -609735
>>>> South Korea
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>>>> Mobile no. - 010-5818-3680
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>>>>
>>>>
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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.
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
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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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