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

From: Pengfei Li <>
Date: Tue, 14 Oct 2014 11:26:44 -0400

Hi Manuel,

I checked your script and found the error may come from that there is no Calcium ion information in the metalParm.xml file and in the metals.xml file there is a wrong type of the Calcium (which named as "CA"),
which will cause confusion (treat the Calcium ion as a carbon atom which has atom type as "CA") when do the modeling.

The following modifications may be help:

(1) Open $AMBERHOME/dat/mtkpp/metals/metals.xml file and replace the fifth line with the following sentence:

      <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="C0" symbol="Ca" kind="0"/>

(2) Open $AMBERHOME/dat/mtkpp/metals/metalParm.xml file and add the following sentence in the middle:

    <entry mass="40.08" name="C0" vdwRadius="0.0" potentialWellDepth="0.0" element="Ca" hybridization="sp3" description="Calcium ...."/>

You can try to run the command again to see whether the problem has been fixed.

All the best,

On Oct 13, 2014, at 7:28 PM, wrote:

> Hi Francois!
> Yes, I am aware of R.E.D., and I've used it before to very good results! Again, my question would be, since the idea is to compare the stability of the metal site in the presence of either Ca or Mn, how comparable do you think would it be, if I use RED for Ca, and MCPB for Mn? Or would you rather recommend that, if I use RED, I do everything with RED?
> Thanks,
> Manuel
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Tue Oct 14 2014 - 08:30:04 PDT
Custom Search