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: Mon Nov 21 2005 - 10:33:44 CST

Dear Jiapu,

> My pdb file is including two chains: chain A and chain B. I
> want link an
> atom in chain A to another atom in Chain B by a bond. Chain A has the
> residues numbered from 119 to 226, and chain B has the same residue
> numbers.
> For example, if I want to link a bond between chainA.residue179.SG and
> chainB.residue214.SG, then how to use xleap's "bond" command?

I believe that inside leap the residue numbers are unique. Leap achieves
this by incrementing by 10,000 (I think) the residue numbers for each chain.
Thus chain A would have residues numbered 1 -> Nres, chain B would have the
residues numbered 10001 -> (10000 + Nres)

So you can do the bonding by say:

> bond MYMOL.179.SG MYMOL.10214.SG

Note the numbering may be slightly different to this. You can use the desc
command to check it.

e.g. desc MYMOL.10214

etc... Note, if you have any other 'molecules' present such as coenzymes
then these will be incremented in residue number as well so that your chain
B may be say 20,000 + Nres etc...

I hope this helps.

All the best
Ross

/\
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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
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