Re: [AMBER] Thermodynamic Integration by using pmemd

From: Ying-Chieh Sun <>
Date: Fri, 11 Jul 2014 20:54:19 +0800

A good place to start is Tutorial A9:
although this is for sander. Then, you can change some to fit pmemd
following JCTC original paper as suggested by Hannes.

Hope this help.


-----Original Message-----
From: Hannes Loeffler []
Sent: Friday, July 11, 2014 6:02 PM
Subject: Re: [AMBER] Thermodynamic Integration by using pmemd

On Fri, 11 Jul 2014 17:33:21 +0800
Sun <> wrote:

> In my calculation by using pmemd, the system contains 120 residues (
> 100 regular amino acids and 20 waters ). The atom numbers are
> unchanged in the start point and end point . When I combined these
> two structures (pdb) into one pdb and then used Leap to generate
> topology and coordinate files, I found that , by default , Leap put
> all water molecules in the last place, e.g. :1-200 are amimo acids
> and :200-240 are water molecules. But what I actually expect is the
> oder like this : :1-120 are amino acids and water molecules
> corresponding to the start pont and :121-240 are the end points.

You only need two sets of coordinates (and eventually topologies) for the
_unique_ atoms. You would need to use masks in the input file to inform
pmemd what those are. The unique atoms define which part will be treated
through dual topolgy and are the atoms that you wish to be transformed
during simulation. Which atoms to include is your choice.
You will have to make sure that the unique atoms are in exactly the same
order in both copies. That's how pmemd knows how to map atoms between
initial and final states.

I guess you want to do something like side-chain mutation. The setup for
this case is explained in 2.3 of the supplement of the original JCTC paper.
You probably want to post-process your topology file with parmed to
eliminate redundant atoms and terms as described there.

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