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
MASS
SJ 32.06
CU 65.36
BOND
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
Jorgen
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Received on Thu Jun 04 2009 - 01:11:01 PDT
