Hi,
I want to build my manganese protein by MCPB program,after I runed sh
genMetalFF.sh -n 1AMP_OH,I looked for the settings file,I found that the
file metals.xml and metalparm.xml does not include the mananese
information,could I execute the next procedure,and I can get the MM
parameters for my manganese protein?
----------------------------metals.xml--------------------------------------
---------------------------------------------
<?xml version="1.0" ?>
<stdLib>
<group identity="metals">
<fragment code="METSM CA" identity="Calcium Ion" symbol=" CA" type="m">
<atom atNum="20" atmCharge="2.0" bond12="-1" bond13="-2" bond14="-3"
bondAngle="90.0" bondLength="1.0" bondTorsion="180.0" chain="M"
identity="C0 " index="1" type="CA" symbol="Ca" kind="0"/>
<alias alias=" C0 " original="C0 "/>
<alias alias=" C0" original="C0 "/>
</fragment>
<fragment code="METSM FE" identity="Iron(II) Ion" symbol=" FE" type="m">
<atom atNum="26" atmCharge="2.0" bond12="-1" bond13="-2" bond14="-3"
bondAngle="90.0" bondLength="1.0" bondTorsion="180.0" chain="M"
identity="FE " index="1" type="FE" symbol="Fe" kind="0"/>
<alias alias=" FE " original="FE "/>
<alias alias=" FE" original="FE "/>
</fragment>
<fragment code="METSM CO" identity="Cobalt(II) Ion" symbol=" CO"
type="m">
<atom atNum="27" atmCharge="2.0" bond12="-1" bond13="-2" bond14="-3"
bondAngle="90.0" bondLength="1.0" bondTorsion="180.0" chain="M"
identity="CO " index="1" type="CO" symbol="Co" kind="0"/>
<alias alias=" CO " original="CO "/>
<alias alias=" CO" original="CO "/>
</fragment>
<fragment code="METSM NI" identity="Nickel(II) Ion" symbol=" NI"
type="m">
<atom atNum="28" atmCharge="2.0" bond12="-1" bond13="-2" bond14="-3"
bondAngle="90.0" bondLength="1.0" bondTorsion="180.0" chain="M"
identity="NI " index="1" type="NI" symbol="Ni" kind="0"/>
<alias alias=" NI " original="NI "/>
<alias alias=" NI" original="NI "/>
</fragment>
<fragment code="METSMCUI" identity="Copper(I) Ion" symbol="CUI"
type="m">
<atom atNum="29" atmCharge="1.0" bond12="-1" bond13="-2" bond14="-3"
bondAngle="90.0" bondLength="1.0" bondTorsion="180.0" chain="M"
identity="CU " index="1" type="U1" symbol="Cu" kind="0"/>
<alias alias=" CU " original="CU "/>
<alias alias=" CU" original="CU "/>
</fragment>
<fragment code="METSM CU" identity="Copper(II) Ion" symbol=" CU"
type="m">
<atom atNum="29" atmCharge="2.0" bond12="-1" bond13="-2" bond14="-3"
bondAngle="90.0" bondLength="1.0" bondTorsion="180.0" chain="M"
identity="CU " index="1" type="CU" symbol="Cu" kind="0"/>
<alias alias=" CU " original="CU "/>
<alias alias=" CU" original="CU "/>
</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 "/>
</fragment>
<fragment code="METSMMO3" identity="Molybdenum(III) Ion" symbol="MO3"
type="m">
<atom atNum="42" atmCharge="3.0" bond12="-1" bond13="-2" bond14="-3"
bondAngle="109.5" bondLength="1.0" bondTorsion="180.0" chain="M"
identity="MO " index="1" type="MO" symbol="Mo" kind="0"/>
<alias alias=" MO " original="MO "/>
<alias alias=" MO" original="MO "/>
</fragment>
<fragment code="METSMMO4" identity="Molybdenum(IV) Ion" symbol="MO4"
type="m">
<atom atNum="42" atmCharge="4.0" bond12="-1" bond13="-2" bond14="-3"
bondAngle="90.0" bondLength="1.0" bondTorsion="180.0" chain="M"
identity="MO " index="1" type="MO" symbol="Mo" kind="0"/>
<alias alias=" MO " original="MO "/>
<alias alias=" MO" original="MO "/>
</fragment>
<fragment code="METSMMO6" identity="Molybdenum(VI) Ion" symbol="MO6"
type="m">
<atom atNum="42" atmCharge="6.0" bond12="-1" bond13="-2" bond14="-3"
bondAngle="90.0" bondLength="1.0" bondTorsion="180.0" chain="M"
identity="MO " index="1" type="MO" symbol="Mo" kind="0"/>
<alias alias=" MO " original="MO "/>
<alias alias=" MO" original="MO "/>
</fragment>
<fragment code="METSM RU" identity="Ruthenium(II) Ion" symbol=" RU"
type="m">
<atom atNum="44" atmCharge="2.0" bond12="-1" bond13="-2" bond14="-3"
bondAngle="90.0" bondLength="1.0" bondTorsion="180.0" chain="M"
identity="RU " index="1" type="RU" symbol="Ru" kind="0"/>
<alias alias=" RU " original="RU "/>
<alias alias=" RU" original="RU "/>
</fragment>
</group>
</stdLib>
--------------------------------------metalparm.xml-------------------------
----------------------------------------------------------------------
<?xml version="1.0" ?>
<parms name="metals">
<types>
<entry mass="55.845" name="FE" vdwRadius="0.0" potentialWellDepth="0.0"
element="Fe" hybridization="sp3" description="FE ...."/>
<entry mass="58.9332" name="CO" vdwRadius="0.0" potentialWellDepth="0.0"
element="Co" hybridization="sp3" description="CO ...."/>
<entry mass="58.6934" name="NI" vdwRadius="0.0" potentialWellDepth="0.0"
element="Ni" hybridization="sp3" description="NI ...."/>
<entry mass="63.55" name="U1" vdwRadius="1.2" potentialWellDepth="0.05"
element="Cu" hybridization="s" description="Cu(I)"/>
<entry mass="63.55" name="CU" vdwRadius="1.2" potentialWellDepth="0.05"
element="Cu" hybridization="s" description="Cu(II), Remenyi, J Comp
chem,23,697"/>
<entry mass="65.40" name="ZN" vdwRadius="1.1"
potentialWellDepth="0.0125" element="Zn" hybridization="sp3"
description="Zn(II), Merz, PAK, JACS,113,8262"/>
<entry mass="95.96" name="MO" vdwRadius="0.0" potentialWellDepth="0.0"
element="Mo" hybridization="sp3" description="Molybdenum"/>
<entry mass="101.07" name="RU" vdwRadius="1.1"
potentialWellDepth="0.0125"element="Ru"hybridization="sp3"description="Ru
..."/>
</types>
</parms>
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Received on Sun Nov 13 2011 - 22:00:02 PST
