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

From: Ken Merz <>
Date: Mon, 13 Oct 2014 08:06:03 -0400

Besides the technical error you might want to try a mixed model - use MCPB for a bonded Mn model and a nonbonded model for Ca. Kennie

On Oct 12, 2014, at 8:00 PM, wrote:

> Dear Amber developers and users,
> 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 Instead, the calcium has been replaced by a carbon.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...
> Thanks very much,
> Manuel
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Received on Mon Oct 13 2014 - 05:30:02 PDT
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