[gmx-users] Amino acid simulation

[Chandan Choudhury]

Thanks Justin. It worked perfectly.

Chandan

--
Chandan kumar Choudhury
NCL, Pune
INDIA


On Tue, Apr 13, 2010 at 1:08 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Chandan Choudhury wrote:
>
>> Hello gmx-users
>>
>> I am trying to simulate an amino acid (say GLN). It can be as a
>> zwitterionic form or uncharged ends. Neither ffamber or ffopls force fields
>> has a complete parameter for them. While in ffamber, I have the
>>
>
> This is not true.  OPLS can handle isolated amino acids, you just have to
> manually choose the termini in pdb2gmx (using -ter).  Use the "zwitterion"
> forms of the termini, since in fact, you have a zwitterion.
>
> -Justin
>
>
>  parameters for CGLU and NGLU, but not for a Glutamine. Do I need to define
>> it there, or there is some way out. If I need to define it, how do I retrive
>> the partial charges.
>>
>> Any insight would be very helpful.
>> Thanks
>>
>> Chandan
>>
>> --
>> Chandan kumar Choudhury
>> NCL, Pune
>> INDIA
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
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