Re: [AMBER] on antechamber

From: David A Case <>
Date: Mon, 2 May 2016 07:56:57 -0400

On Sun, May 01, 2016, Brett wrote:
> Is any on-line tutorial-like document on how to check the antechamber
> produced files by hand? And what is the fucntion for the ligand-only md
> for checking the antechamber produced files?

Ligand-only md is done the same way as any other md simulation. You can see
if the distributions of conformations matches any information you have about
what the ligand should be doing.

If antechamber seems not to be accurate enough for your purposes, you will
probably need to run quantum electronic structures calculations to map out
(parts of) the potential energy surfaces. The nature of the calculations
neeeded here depends a lot on the nature of the ligand, and there is no simple
general procedure to follow.


AMBER mailing list
Received on Mon May 02 2016 - 05:00:03 PDT
Custom Search