Your question is rather vague. This could be a hard problem, or an easy
one, depending on how far you want to take the parameter development and
how unlike a typical peptide your system is.
What to do here is to decide on what, if any parameters you want to keep
from existing force fields. There are two types of parameters: charges and
bonded parameters, to worry about. Van-der Waals parameters you can
probably hold over from the existing force fields for the atom types that
antechamber will assign or that you borrow from an existing protein force
field.
You will need to develop a set of conformations of your molecule for both
charges and for bonded parameters. Then you will run QM calculations to
perform RESP or IPolQ charge fitting, followed by bonded parameter
fitting. This can be a lengthy process, depending on how long you are
willing to give it. The alternative is to let something like antechamber
assign your parameters from GAFF, study existing force fields and assign
other parameters that it may not know how to fill in.
Tutorials for the more involved way are here:
http://ambermd.org/tutorials/advanced/tutorial28/index.php
http://ambermd.org/tutorials/advanced/tutorial32/index.php
Dave
On Tue, May 12, 2020 at 8:38 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
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Received on Tue May 12 2020 - 09:00:01 PDT
