AMBER Archive (2004)

Subject: AMBER: bond between two polypeptides

From: Jagdish Rai (jagdish_at_icgeb.res.in)
Date: Tue Sep 14 2004 - 03:19:48 CDT

dear sir
 i want to ask following question
the tleap program refused to make bond between two polypeptides in a PDB
file which has a TER line next to last atom line of first polypeptide
bond ss3.10.SG ss3.20.SG
bond: Argument #2 is type String must be of type: [atom]
usage: bond <atom1> <atom2> [order]
but if i remove this TER line it can make a disulfide bond together with
this in energy minimisation the two polypeptides are considered to be
bonded by peptide bond between last amino acid of fist polypeptide and
first amino acid of second polypeptide
how can i make a disulfide bond between two polypeptides

sincierly jagdish rai
malaria lab
ICGEB
INDIA

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