Dear AmberUsers,
I am trying to generate metal site parameters. I have a cysteine in the
metal site and the sulphur of cysteine coordinates with the metal ion. As,
a result I have to rename CYS to CYM, since it interacts with a metal.
However when i see the atom type of Sulphur for both CYS and CYM in the
amino94.xml file they are the same, SH but their atm charge values are
different. Is this a bug. How can MCPB differentiate between two atom types
with the same name????
for CYM
<atom atmCharge="-0.736" bond12="5" bond13="3" bond14="1" bondAngle="116.0"
bondLength="1.81" bondTorsion="180.0" chain="E" identity=" SG " index="8"
type="SH" />
for CYS
<atom atmCharge="-0.3119" bond12="5" bond13="3" bond14="1"
bondAngle="116.0" bondLength="1.81" bondTorsion="180.0" chain="S"
identity=" SG " index="8" type="SH" />
Regards
Ashwini
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Received on Fri Mar 23 2012 - 00:00:04 PDT
