AMBER Archive (2007)

Subject: AMBER: LEaP bond problem

From: Beale, John (jbeale_at_stlcop.edu)
Date: Wed Nov 07 2007 - 06:57:30 CST

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
states:
 
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
problem?
 
Thanks!
 
John
 

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