AMBER Archive (2005)

Subject: RE: AMBER: How to use XLEAP to link one atom in a monomer to another atom in another monomer? (where both the 2 monomers are in a same pdb file)

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sun Nov 20 2005 - 23:59:18 CST

Dear Jiapu,

> How to use XLEAP to link one atom in a monomer to another atom in
> another monomer (where both the 2 monomers are in a same pdb file)?

You can do this in several ways. Two of the simplest are to either manually
bond the relevant atoms using the bond command in Leap. Alternatively, if
you molecule is small enough to be traced visually you can edit it in Xleap
and manually draw in the bonds you want.

The following tutorial covers building a non standard residue and using the
bond command:

http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_four_orig/inde
x.htm

All the best
Ross

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|\oss Walker

| Department of Molecular Biology TPC15 |
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