Hi Amani,
Please treat all the ZN residue with residue name and atom name all as “ZN” in your PDB file (not “ZN1” or “ZN2”) for MCPB.py to recognize it as an metal ion. And you just need to have one ZN.mol2 file containing one ZN ion in order for MCPB.py to know the charges for both of the two ZN ions (since they have the same charge).
BTW, for *ALL* the MCPB.py users, please read the section of “1. Prepare the PDB and mol2 files (effort: < 1 hour):” in the MCPB.py tutorials carefully (http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm> and http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm>) when using MCPB.py. A lot of questions have been asked can be avoided if you read this part carefully. And in this way it will save both your and my time.
Kind regards,
Pengfei
> On Sep 21, 2017, at 11:36 AM, Amani Eshtiwi <eshtiwia2017.gmail.com> wrote:
>
>
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Received on Sat Sep 23 2017 - 15:30:02 PDT
