[AMBER] MCPB.py and MMPBSA issue

From: 庄灿波 <zhuangcb13.mails.jlu.edu.cn>
Date: Sat, 26 Nov 2016 17:32:53 +0800(CST)


   I followed the tutorial 20 and used MCPB.py to creat the charges and
   parameters for my HEME and a ligand.

   And I checked the mol2 file of ligand. The charges of ligand are not

   And there are some parameters (such as bond, angle) between ligand and FE.

   I want to use the parameters created by MCPB.py to calculate MMPBSA.

   Is the calculated MMPBSA value reasonable as the charges are not integer and
   some parameters between ligand and FE?

   The other question is about the tutorial 20 about creating HEME parameters.

   In this tutorial the total charges of HEM.mol2 file are zero, however, the
   charges of protoporphyrin are -4. In my protein, I set the charges of
   protoporphyrin. Is it correct?

   I am looking forward your replay.

   Thank you,

   Canbo Zhuang


   1. http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy_heme.htm
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Received on Sat Nov 26 2016 - 01:30:02 PST
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