AMBER Archive (2009)

Subject: Re: [AMBER] non standart residue library creation with tleap (Zn atom)

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Tue Nov 17 2009 - 14:10:03 CST

Dear Andrey,

> The point is that tutorial is for xleap and I в like to find the
> similar one for tleap. The tutorial refers to GUI only there.

There are only few differences between xLEaP & tLEaP...

You can find information about using LEaP from our tutorials @
http://q4md-forcefieldtools.org/Tutorial/

& you will find information about using .mol2 files as FF libraries in LEaP:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#15
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php
http://q4md-forcefieldtools.org/Tutorial/P2N/All-frag-Pept/script1.cmd
etc...

You will find information about commands available in xLEaP which were
incorporated in tLEaP by our group:
http://q4md-forcefieldtools.org/Tutorial/leap.php

You will find many tLEaP script examples (more or less complex) in
R.E.DD.B. as well as in R.E.D. and R.E.D. Server tutorials:
Organic molecules:
http://q4md-forcefieldtools.org/REDDB/up/W-46/
http://q4md-forcefieldtools.org/REDDB/up/W-46/script1.ff
Standard nucleic acid:
http://q4md-forcefieldtools.org/REDDB/up/F-60/
http://q4md-forcefieldtools.org/REDDB/up/F-60/script1.ff
Non-standard amino-acids:
http://q4md-forcefieldtools.org/REDDB/projects/F-75/
http://q4md-forcefieldtools.org/REDDB/projects/F-75/script1.ff
See F-81 as well
Glyco-conjugates:
http://q4md-forcefieldtools.org/REDDB/projects/F-71/
http://q4md-forcefieldtools.org/REDDB/projects/F-71/script1.ff
http://q4md-forcefieldtools.org/REDDB/projects/F-72/
However, F-72 is still protected
http://q4md-forcefieldtools.org/REDDB/projects/F-84/
http://q4md-forcefieldtools.org/REDDB/projects/F-84/script1.ff

and even more...

regards, Francois

> 17.11.09, 10:57, "Jason Swails" <jason.swails_at_gmail.com>:
>
>> Yes. All xleap does is provide a visualization option so that you can see
>> and manipulate your system in an x-window. Any command you can do in xleap
>> (except edit) can be done in tleap.
>> Good luck!
>> Jason
>> On Tue, Nov 17, 2009 at 10:47 AM, Andrew Voronkov wrote:
>> > Dear Amber users,
>> > how can I make non-standart residue library without xleap. Is it possible
>> > to do it only withtleap usage?
>> >
>> >
>> http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_four/section2.htm
>> >
>> > Sincerely yours,
>> > Andrey

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