Re: [AMBER] Multiple MEPs option in R.E.D tools

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 31 Mar 2015 16:53:52 -0400

On Tue, Mar 31, 2015 at 3:07 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:

> Dear Yip Yew Mun,
>
> > I can't help you with #1, but the answer to #2 is yes. Resp on its own
> > can take in multiple orientations/conformations and fit them
> > simultaneously. You can get some detail on this from the A1 tutorial on
> > the AMBER site
> > (http://ambermd.org/tutorials/advanced/tutorial1/section1.htm).
> > To answer your specific question, you need to extract just the ESP
> > information from the gaussian file (see esp.sh) and then simply
> concatenate
> > those bits of ESP into a single file.
>
> Some time ago there were 'some' discussions about this tutorial: I
> have no problem writing - rewriting - repeating -
> whatever_is_the_world_used_here that I do not agree with the charge
> derivation procedure, which is presented in this tutorial: I do not
> think this approach should be followed by a new user.
>

‚ÄčAt the end of the day, it's a multi-conformational RESP fit using a
HF/6-31G*-derived MEP, which fits the prescription for the Merz-Kollman
charge derivation scheme. It also shows users how resp works, which they
can then take and extend to include multiple orientations, for instance.

There is value to providing a workflow that can be scripted and run on a
computer in which all components of the workflow can be downloaded and
installed locally. The perl RED scripts are candidates, but you regularly
discourage their use in favor of a solution that is only available through
a web interface.

All the best,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Mar 31 2015 - 14:00:02 PDT
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