Sorry for my poor english, but i think the most difference between CYM
and CYS is that there is no H atom bond to S atom, so if you choice CYM
as the residue name, the parameters of the CYM will be used by TLEAP(or
XLEAP). And MCPB will assign new charge and force field parameters for
the Metal binding group.
On 03/23/2012 02:39 PM, ashwini gupta wrote:
> 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 - 02:30:03 PDT
