[gmx-users] Amino acid simulation

Justin A. Lemkul jalemkul at vt.edu
Mon Apr 12 21:38:22 CEST 2010

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.
> Thanks
> Chandan
> --
> Chandan kumar Choudhury
> NCL, Pune


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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