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

[R C Dash]

Have you tried swissparam.ch server (charmm ff) or vienna.ptm.univie.ac.at
server ( gromos ffg45a3, ffg45a7 and ffg54a8 ff) for beta alanine

On Oct 12, 2017 7:16 PM, "Justin Lemkul" <jalemkul at vt.edu> wrote:



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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