On the practical side, if you’re talking about a somewhat long molecule that has repeating residues, there is a program called prepgen in AMBER that might be what you need.
You cut up your peptide into residues, and parametrize each of them, like from gaff, or the more accurate QM model like what Dave just mentioned. Prepgen will give you a prepi file that has the parameters readable by tleap.
Then when you load your molecule into tleap, you load the prepi also.
The Amber manual has the exact details, and also a sample file for using prepgen. Pointing you in this direction if that’s what you may need.
Sent from my iPhone
> On May 12, 2020, at 7:38 AM, Rana Rehan Khalid <ray.binm.gmail.com> wrote:
>
> Dear amber users
>
> Could you please guide me how I can parameterize a peptide-like compound
> is there any tutorial available. Thanks
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed May 13 2020 - 00:30:03 PDT
