Here is a supplement:
For the Calcium ion, you can use the VDW parameters we determined in the following paper:
http://pubs.acs.org/doi/abs/10.1021/ct400146w
On Oct 14, 2014, at 11:26 AM, Pengfei Li <ambermailpengfei.gmail.com> wrote:
> 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,
> Pengfei
>
> On Oct 13, 2014, at 7:28 PM, mmaestre.gate.sinica.edu.tw 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
>>
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>
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Received on Tue Oct 14 2014 - 09:00:02 PDT
