Re: [AMBER] Thermodynamic Integration using PMEMD

From: Roma Mukhopadhyay <>
Date: Fri, 18 Aug 2017 13:34:32 +0000


I did go through the A9 tutorial, and got the idea of how to setup the pdb file.

Attached are the pdb file, the leap file, the prmtop and inpcrd file.

So I had created the pdb file containing both molecules separated by TER card. Then I got the single prmtop and inpcrd file using the tleap. Each molecule has 25 atoms, however when I run minimization, the program is recognizing 50 atoms of one atom, instead of recognizing 25 atoms for each molecule. In my minimization steps i did use timask flags.

How do I overcome this problem?



From: Hannes Loeffler <>
Sent: Friday, August 18, 2017 7:09:45 AM
Subject: Re: [AMBER] Thermodynamic Integration using PMEMD

On Thu, 17 Aug 2017 18:24:00 +0000
Roma Mukhopadhyay <> wrote:

> Hi all,
> I want to do the pKa Tutorial as in
>, but i
> want to use Pmemd instead of Sander.

Have a look into the A9 tutorial to get and idea how TI/FEP works with

> But I am having trouble with the leap program not being able to
> understand the two separate molecules.

You would need to provide full details here before anyone will be able
to help you.


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Received on Fri Aug 18 2017 - 07:00:03 PDT
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