[gmx-users] Regarding beta-alanine amino acid molecule in charmm 36 FF

Justin Lemkul jalemkul at vt.edu
Fri Oct 13 01:16:26 CEST 2017

On 10/12/17 5:03 AM, Dilip H N wrote:
> Hello,
> 1] I wanted to simulate beta-alanine amino acid. Since i am using charmm 36
> FF for simulation of other molecules too, so prefer using the same
> Forcefield.
> But i tried searching in the .rtp file, but only alanine  [ALA] amino-acid
> is there...but not beta-alanine. So i am not able to find it in charmm 36
> FF ...
> So can anybody help/suggest on how to solve this issue..

There are no official CHARMM parameters for beta-alanine. Search the 
literature to see if someone has derived something suitable.

> 2] How can i find the required molecule in the .rtp file..?? since its full
> name is not written in the file.for eg., what is [ 11BPO ]..?? which
> molecule does it represent..?? etc...

Refer to the original CHARMM residue topology files (.rtf), available 
from the MacKerell lab webpage. These contain full molecule names and 
structural drawings.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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