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Hi Ben,
I am very luck and pleasure to get your instant reply.As you refered in
your first mail,van der Waals parameters of the Manganese I have obtained by
the website
http://www.pharmacy.manchester.ac.uk/bryce/amber(you may take a
look at the attachment).Although I have obtained the parameter with MN2+,I
don't know how to change these MN2+ parameters into metalparm.xml(like zn
<entry mass="65.40" name="ZN" vdwRadius="1.1" potentialWellDepth="0.0125"
element="Zn" hybridization="sp3" description="Zn(II), Merz, PAK,
JACS,113,8262"/>) and metals.xml(like zn </fragment>
<fragment code="METSM ZN" identity="Zinc(II) Ion" symbol=" ZN" type="m">
<atom atNum="30" atmCharge="2.0" bond12="-1" bond13="-2" bond14="-3"
bondAngle="90.0" bondLength="1.0" bondTorsion="180.0" chain="M"
identity="ZN " index="1" type="ZN" symbol="Zn" kind="0"/>
<alias alias=" ZN " original="ZN "/>
<alias alias=" ZN" original="ZN "/>).
I also would like to need your advises,because I encounter some new
problems:
(1) when I created the side chain model by hand,I dont know how to add the
ligand with a small molecule that has three oxygen coordnated with two MN2+
in the *_sidechain.bcl.If I dont add the ligand information in that file.
(2) I also runed successfully MCPB -i *_sidechain.bcl -l
*_sidechian.bcl.log.The log showed that MCPB Exited Normally,I can get the
two files with *_sidechain_fc.com and *_sidechain_opt.com,habe these two
files been optimised by gaussian?
Best
Regards
JiYuan
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Received on Mon Nov 14 2011 - 19:30:03 PST
