AMBER Archive (2009)

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

From: Andrew Voronkov (drugdesign_at_yandex.ru)
Date: Wed Nov 18 2009 - 07:19:58 CST

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

ok for this tutorial http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_four/section2.htm
I need the edit option in xleat, what is the analog in tleap where I can
Edit->Edit Selected Atoms

"You should now go through and assign an atom type and charge for all of the atoms in the unit, in this case just the copper atom. We will select CU for the copper atom type, this is not currently in use. Once this is done we can select Table->Save and Quit. "

Your tutorials are about RESP chareges and I actually don t need RESP charges here, only non Zn atom specification using tleap but not GUI of xleap.

Best regards,
Andrew

> 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" :
> >
> >> 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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