[gmx-users] Amino acid simulation
iitdckc at gmail.com
Tue Apr 13 11:57:44 CEST 2010
Thanks Justin. It worked perfectly.
Chandan kumar Choudhury
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.
> 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.
>> Chandan kumar Choudhury
>> NCL, Pune
> 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
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