Venkat,
if you have parm99 parameters available for your ligand, that is good
news. The approach to substitute missing parameters by gaff equivalents
is also ok IMO.
I'd suggest, however, at least some test simulations of the isolated
ligand system prior to starting the large protein simulation to ensure
that the structure and dynamics of the system is as expected.
Regards,
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
Gemany
Am 19.11.2021 um 07:07 schrieb Venkatareddy Dadireddy:
> 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 Fri Nov 19 2021 - 03:30:02 PST
