[gmx-users] Regarding ffG43a1p force field

Thu Jun 23 09:12:11 CEST 2011

ok sir..

On Thu, Jun 23, 2011 at 4:06 PM, Ramachandran G <gtrama at gmail.com> wrote:

> 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 ...
>>>>>>
>>>>>> --
>>>>>> 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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>>
>>
>>
>> --
>> 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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