AMBER Archive (2009)
Subject: Re: [AMBER] (no subject)

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Mon Jun 08 2009 - 12:14:05 CDT

Previous message: David A. Case: "Re: [AMBER] Can we define +1 or -1 charge for an organic drug using GAFF?"
In reply to: Vishal Maingi: "[AMBER] (no subject)"
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Dear Vishal,

> in amber is there any option of loop to be used in polymer
> building. can I use any loop command ,if there, to grow the polymer
> further using my own residues stored in abc.lib file
> another question is regarding the branched polymer building. is
> there any option to build the polymer by branching along with linear
> growth although linear growth can be done.

You will find examples of LEaP scripts in R.E.DD.B. as well as in Tutorials @
http://q4md-forcefieldtools.org/

See for instance:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php

- For amino-acids:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
With the corresponding LEaP script:
http://q4md-forcefieldtools.org/Tutorial/P2N/All-frag-Pept/script1.cmd
- For nucleotides:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
With the corresponding LEaP scripts:
http://q4md-forcefieldtools.org/Tutorial/P2N/All-frag-Nuc/script1A.cmd
http://q4md-forcefieldtools.org/Tutorial/P2N/All-frag-Nuc/script1B.cmd
- For _branched_ glycoconjugates:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#26
With the corresponding LEaP script:
http://q4md-forcefieldtools.org/REDDB/projects/F-71/script1.ff

regards, Francois

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Previous message: David A. Case: "Re: [AMBER] Can we define +1 or -1 charge for an organic drug using GAFF?"
In reply to: Vishal Maingi: "[AMBER] (no subject)"
Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]

AMBER Archive (2009)Subject: Re: [AMBER] (no subject)

AMBER Archive (2009)
Subject: Re: [AMBER] (no subject)