Re: [AMBER] (no subject)

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Mon, 8 Jun 2009 18:14:05 +0100

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

See R.E.DD.B. projects:
http://q4md-forcefieldtools.org/REDDB/projects/W-46/
http://q4md-forcefieldtools.org/REDDB/projects/W-46/script1.ff
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-74/
http://q4md-forcefieldtools.org/REDDB/projects/F-74/script1.ff
http://q4md-forcefieldtools.org/REDDB/projects/F-81/
http://q4md-forcefieldtools.org/REDDB/projects/F-81/script1.ff
http://q4md-forcefieldtools.org/REDDB/projects/F-82/
http://q4md-forcefieldtools.org/REDDB/projects/F-82/script1.ff

regards, Francois



_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jun 09 2009 - 01:12:09 PDT