AMBER Archive (2006)

Subject: Re: AMBER: converting from parm to parm7

From: Raffaella D'Auria (rdauria_at_uci.edu)
Date: Tue Jul 25 2006 - 11:00:50 CDT

Hello,

I have no problem using the parm6 to run with amber8 (the version of amber
I am using). What I was trying to do, when I ask the question, was to
recover the force field parameters used in the past from the parm6 I had.
I can enter the file and manually look up the values, the only
inconsistency I found was in the value and ordering of the Lennard-Jones A
and B parameters... accordingly I have posed my question to the list since
I can't recall how to go from r and epsilon to A and B (help in this
direction is still needed) and I was hoping to use leap to convert from
one format to the other to see whether the inconsistency would disappear.
I apologize for having been a bit obscure in my original posting and I
hope I made myself clearer now.

Thanks :)

Raffaella.

On Sun, 23 Jul 2006, David A. Case wrote:

> On Fri, Jul 21, 2006, Raffaella D'Auria wrote:
> >
> > I was wondering if anyone is aware of a way to convert an old parm.top
> > file into the new parm7 format.
>
> I'd be interested to know why this conversion is necessary. All Amber
> programs should be able to auto-detect and read either format. If there
> is an Amber program that is not doing this correctly, we should try to fix it;
> if it is a third-party program, I'd be interested to know which one it is.
>
> ...thx...dac
>
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____________________________________________________________________
Raffaella D'Auria, PhD | e_mail: rdauria_at_uci.edu
Department of Chemistry |
3218 Natural Sciences 1 | ph. n.: 949-824-9921
University of California, Irvine |
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