Lara,
most probably you'll want to choose an approach similar to that
described in the Amber tutorial about parameterizing a non-standard
amino-acid residue:
https://ambermd.org/antechamber/pro4.html
(Unless your Lys-Plp is a standalone moiety in your case.)
There are many publications about parameterization of non-standard
amino-acids; see the work of the Floudas group
dx.doi.org/10.1021/ct400556v
as an example.
Maybe that helps.
Best,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
On 02/08/2022 09:01 PM, Lara rajam wrote:
> Dear AMBER,
> Sorry for posting it again - I have not got any insight!
> I am interested in generating a simulation for PLP linked LYS for my
> protein.
> I have gone through the forum and got the same question asked in 2018
> ( http://archive.ambermd.org/201803/0040.html). But I am not able to find
> the solution for it. Can anyone let me know what needs to be done?.
>
> Can I follow the non standard residue tutorial? If so , how do I need to
> take the combined residue atoms for Gaff ?
>
> Any information will be appreciated.
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>
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Received on Wed Feb 09 2022 - 12:30:02 PST
