[AMBER] Query regarding the MCPB.py workflow

From: Abhi Acharya <abhi117acharya.gmail.com>
Date: Sat, 12 Nov 2016 14:39:19 +0530

Hi amber users,

I am trying to use the MCPB.py workflow to derive parameters for an active
site containing Cu2+ and Ca2+ ions. The Cu2+ ion is coordinated by two
water molecules, and active site residues Asp, His etc.
My question is that in the input file for MCPB.py do we need to specify
separate mol2 files for the two water molecules and the coordinating
residues? In the MCPB.py tutorial at this link:
http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm the input file
does not specify any of the coordinating His residues. But still in the 3rd
step i.e. MCPB.py -i 1OKL.in -s 3, the tutorial says that mol2 files for
HD1, HD2 and HE1 will be created. I am a bit confused.

I request you to kindly clarify this.

Thanks and Regards,
Abhishek Acharya
CFTRI, Mysore.
AMBER mailing list
Received on Sat Nov 12 2016 - 01:30:02 PST
Custom Search