Re: [AMBER] Calcium possibly replaced by carbon with MCPB

From: FyD <>
Date: Mon, 13 Oct 2014 21:40:29 +0200

Dear Manuel,

you might be interested in using R.E.D. Server Dev./PyRED - all the
elements of the periodic table are handled...

regards, Francois

> For the last couple of days, I have been trying to parameterize a
> metal binding site with MCPB. The binding site can be occupied
> either by calcium, or by manganese. The manganese parameterization
> has run like a charm (up until now... I'm still waiting for the
> point charge calculation to finish), but the calcium one is giving
> me problems while preparing the files for the force constant
> calculation.
> I'm using the following lines to define the calcium and its bonds:
> # Create non-standard residue library
> copyStdResidue metals/.CA NAME/PA1
> # Create PA1-7 from CA-1
> createResidue PA1 in CLR
> addToResidue /NAME/CLR/PA1 /NAME/1/.CA-1/C0..
> # Create bonds with Ca
> createBond /NAME/CLR/PA1/C0.. /NAME/CLR/AS1/.OD2
> createBond /NAME/CLR/PA1/C0.. /NAME/CLR/AS2/.OD1
> createBond /NAME/CLR/PA1/C0.. /NAME/CLR/GL1/.O..
> createBond /NAME/CLR/PA1/C0.. /NAME/CLR/AN1/.OD1
> createBond /NAME/CLR/PA1/C0.. /NAME/CLR/OH1/.O..
> createBond /NAME/CLR/PA1/C0.. /NAME/CLR/OH2/.O..
> Now, I run MCPB with the sidechain.bcl file, I obtain a settings
> file which tells me that PA1 is a metal:
> <fragment identity="Calcium Ion" symbol="PA1" code="METSMPA1" type="m">
> <atom identity="C0 " index="1" type="CA" chain="M"
> atmCharge="2" bond12="-1" bondLength="1" bond13="-2" bondAngle="90"
> bond14="-3" bondTorsion="180" kind="0" bType="1" bTop="0" bKind="0" />
> <alias original="C0 " alias=" C0 " />
> <alias original="C0 " alias=" C0" />
> </fragment>
> </group>
> But when I open the pdb file, the sdf file, and the mol file, there
> is no metal atom. Instead, the calcium has been replaced by a
> carbon. I'm not quite sure what is happening, but my guess is that,
> at some point, the "CA" type gets understood as C-alpha, instead of
> Calcium. I'd really appreciate some help with this, because I am
> really puzzled by the problem...

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Received on Mon Oct 13 2014 - 13:00:02 PDT
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