Dear Dr. Anselm Horn,
I am sorry to mention that these (SAM) parameters were generated to be
compatible with AMBER99 ff and used with amber99ff in gromacs package.
But finally, I got a paper<
https://pubs.rsc.org/en/content/articlelanding/2018/cp/c7cp07265a> where the authors have the same parameters
mentioned above and provided the frcmod file (please find the attachment) for SAM.
Three dihedral parameters needed attention (ATTN, need revision). I replaced
these dihedral parameters with parameters obtained from gaff. Similar approach
was used in amber tutorial<
http://ambermd.org/tutorials/basic/tutorial5/> (green fluorescence protein). Please correct me if my
approach is wrong.
In my system (methyltransferase), I am interested in loop dynamics around
the active site where SAM also sits. SAM does not have much influence on
these loop dynamics (I assume).
Thank you,
Venkat
________________________________
From: Dr. Anselm Horn <anselm.horn.fau.de>
Sent: Thursday, November 18, 2021 1:38 PM
To: amber.ambermd.org <amber.ambermd.org>
Subject: Re: [AMBER] S-adenosyl-L-methionine (SAM) ff parameters
External Email
Venkat,
I doubt that you can simply 'convert' the Gromacs parameters into the
Amber world, since probably different force fields are used.
Maybe you could use the Gromacs parameterization and its description as
template in the sense that critical parameters are identified there. At
the end, however, it depends on your research aims which level of detail
you want to apply to the respective parameterization.
Regards,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Germany
On 11/13/2021 05:53 AM, Venkatareddy Dadireddy wrote:
> Dear Amber Users,
>
> I need S-adenosyl-L-methionine parameters.
> I found one from a paper: "A consistent S-Adenosylmethionine force field improved by dynamic Hirshfeld-I atomic charges for biomolecular simulation". The authors have provided parameters
> in the form of *.itp (include topology) file to use with Gromacs. But I want to use with Amber package.
> How to extract the parameters to use with Amber. I want to prepare library (*.off) and frcmod files from
> *.itp (please find with attachment).
> Please guide me.
>
> Thank you,
> Venkat
>
>
>
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Received on Thu Nov 18 2021 - 22:30:03 PST
