AMBER Archive (2009)

Subject: RE: [AMBER] help

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Fri Jun 12 2009 - 11:02:06 CDT

Hi 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 can only have one head or tail atom in a residue within leap so your
options are either to make the system one large residue or to use the bond
command to add in the missing bonds. In the later case it should be fairly
easy to write a script to do this and then just source that within leap.

Good luck,
Ross

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|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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