AMBER Archive (2008)

Subject: Re: AMBER: files in Amber directory ( to Junmei Wang )

From: Junmei Wang (junmwang_at_gmail.com)
Date: Thu Jul 17 2008 - 09:56:06 CDT

Hi, John,
Antechamber is designed to work with molecules having no open valence. But
if no atom type and bond type assignments and charge calculations are
involved, antechamber can be used to to handle molecules with open valences.
For your molecules, you could generate mol2 or ac files, manually assign
atom types, and generate prepi files using antechamber if you want to. For
the force field parameters, you may run parmchk to find the missing
parameters and print out all the force field parameters using the "-a" flag.
If you want to use OPLS-UA, you need to assign atom types based on the atom
type definitions of OPLS-UA and loading the OPLS-UA parmameter file with the
"-p" flag when running parmchk (the default is gaff.dat). You cannot change
the functional form for the current Amber packages.

Best

Junmei

2008/7/15 John Bennett <john.bennett_at_ymail.com>:

> Dear Wang,
>
> I'm using Amber 9 v. I'm interested in n-alkanes and evaluating
> thermophysical and structural properties of n- alkanes and binary
> mixtures of n-alkanes. I examined all the files in Amber directory and saw
> some files called OPLS. And I am planning to modify gaff and use OPLS-UA
> force fields for my molecular structure. I wonder if I can use OPLS-UA
> force field using Antechamber. So I need to know some extra information
> about this issue and need some expert advice and suggestions. I thought
> that you can help and also lead me to do the right thing. As you know GAFF
> and OPLS-UA have different functional forms and force constants. I can edit
> charge info and use my own force field parameters. I think it is also need
> to use the right functional forms and force constants . Am I right? How can
> I change and edit the functional forms and force constants of GAFF force
> field ? Where are the functional forms and force constants information of
> force fields in Amber directory? . In this sense, I'm waiting for your
> contributions.
>
>
>
> Sincerely,
>
>
>
>

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