AMBER Archive (2009)

Subject: Re: [AMBER] Residues

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Fri Jun 12 2009 - 09:24:35 CDT

Dear Kirtana,

> Is it possible to connect the residues with multiple connectivity using
> xleap.I would like to know if I have multiple tails in each of my residue
> how should I use it in the mainchain.dat file and make the connectivity in
> xleap.I referred it from the tutorial
> http://ambermd.org/antechamber/dna.htm

You might be interested in looking as well @
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#26

With the corresponding LEaP script defining tails and queues for
branched systems:
http://q4md-forcefieldtools.org/REDDB/projects/F-71/script1.ff
also available from
http://q4md-forcefieldtools.org/REDDB/projects/F-71/

Another good example is also the CYX residue in the Amber force field
topology database:
xleap -f leaprc.ff99
desc CYX
desc CYX.1

regards, Francois

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