AMBER Archive (2007)

Subject: Re: AMBER: prepin file format description; pointers on parameterization

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Thu Oct 25 2007 - 00:14:32 CDT

Quoting David Mobley <dmobley_at_gmail.com>:

> On 10/24/07, FyD <fyd_at_q4md-forcefieldtools.org> wrote:
>> For mol2 file format you could see the following pages:
>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php
>> and in particular:
>> -I.3.3- The Tripos mol2 file format @
>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#15
>> Please, see also the new "savemol2" command incorporated in LEaP
>> -I.3.3.5- Using Tripos mol2 files in LEaP: Implementation of new
>> features in LEaP @
>> http://q4md-forcefieldtools.org/Tutorial/leap.php
>
> This is really confusing. Which version of leap are you referring to
> that has a savemol2 command? There is no such command in my (very
> recent) version of leap.

Did you read the tutorial ?

In the introduction, it is written:

This tutorial describes the use of the Tripos mol2 file format in the
LEaP program (available in the AMBER program distribution and soon in
the AMBER tools), and the conversion of a mol2 file into an AMBER OFF
library. To this purpose, new commands have been implemented in LEaP
and a perfect compatibility between R.E.D., R.E.DD.B. and LEaP is now
observed. The complete description of these new commands is reported
below along with examples.

regards, Francois

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