[AMBER] Thermodynamic Integration using PMEMD

From: Roma Mukhopadhyay <roma1988.nmsu.edu>
Date: Thu, 17 Aug 2017 18:24:00 +0000

Hi all,

I want to do the pKa Tutorial as in http://ambermd.org/tutorials/advanced/tutorial6/section1.htm, but i want to use Pmemd instead of Sander. Based on the manual I understand that for Pmemd we need to have one pdb file containing both molecules, separated by a TER card for obtaining a single prmtop and inpcrd files respectively. But I am having trouble with the leap program not being able to understand the two separate molecules. How can I achieve that?
I would really appreciate a detailed outline as to how to do this same tutorial using pmemd.

Have a good day ahead.


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Received on Thu Aug 17 2017 - 11:30:03 PDT
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