[gmx-users] Amino acid simulation

Tamas Horvath hotafin at gmail.com
Mon Apr 12 20:53:08 CEST 2010

It's highly unusual to simulate a single amino acid. I don't exactly know
what's your purpose with it, but if you really want to do it, you need to
generate those parameters.
I know there are web services for generating gromos FF parameters for
"unusual" molecules, possibly there are such resources for amber or opls

On Mon, Apr 12, 2010 at 8:36 PM, Chandan Choudhury <iitdckc at gmail.com>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 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
> --
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