AMBER Archive (2009)

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

From: Jason Swails (jason.swails_at_gmail.com)
Date: Tue Nov 17 2009 - 12:05:05 CST


Andrey,

If you look up the leap commands in the ambertools manual, you can find
text-based commands to do anything you want. The commands that work in
xleap also work in tleap, except the edit command. To add a charge in
tleap, use the "set charge <chargevalue> <atom>" command and to define head
(0) and tail (1) atoms, use the set connect0 and set connect1 commands. The
manual should tell you how to do it. You do not need xleap to do the
tutorial.

Good luck!
Jason

2009/11/17 Andrew Voronkov <drugdesign_at_yandex.ru>

> The point is that tutorial is for xleap and I like to find the similar
> one for tleap. The tutorial refers to GUI only there.
>
> Best,
> Andrey
>
> 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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> > > AMBER_at_ambermd.org
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> > >
>
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-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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