AMBER: LEaP bond problem

From: Beale, John <>
Date: Wed, 7 Nov 2007 06:57:30 -0600

I have a protein with a serine at the active site. The serine is residue
53 and the ser-OH is designated OG. I want to bind the serine-OG to the
phosphorus of a phosphonate ligand. The ligand is residue 500 and the
phosphorus is designated P. I would like to bond OG to P. In xleap I
enter "bond blh.53.OG blh.500.P". I am getting an error message that
bond: Argument #2 is type String must be if type: [atom]
usage: bond <atom1> <atom2> [order]
Can someone tell me what I am doing wrong and how I can correct this

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Nov 11 2007 - 06:07:07 PST
Custom Search