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

[Justin Lemkul]

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

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

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