AMBER Archive (2009)

Subject: [AMBER] creating bond

From: Jorgen Simonsen (
Date: Wed Jun 03 2009 - 12:04:11 CDT

Hi all,

I have a problem that I would like to create bonds between an ion and
different residue in a protein simulation. I have create lib-files and for
my methionine I have included the Cu-ion but I have a cys residue as well
that I would like create a bond between the Cu-ion and the sulfur but it
seems that it doesn't recognize the bond.

In the lib file my copper is included in the MEM residue like this

 "CU" "CU" 0 1 131075 18 29 0.289000

and for the sulfur in my Cys it looks like this

 "SG" "SJ" 0 1 131072 8 16 -0.28400

I then create a frcmod file with bond parameters etc like this for the
copper interaction
## Modification
SJ 32.06
CU 65.36

SJ-CU 5010.62 1.18
CU-SJ 5010.62 1.18
CT-SJ 203.0 2.21

it can recognize the CT-SJ bond from this file if I increase the force
constant to 2500 but it cannot recognize the SJ-CU - Any help or hinits
appreciated thanks in advance

Best regards

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