Re: [AMBER] Thermodynamic Integration by using pmemd

From: Hannes Loeffler <>
Date: Fri, 11 Jul 2014 11:01:57 +0100

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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Received on Fri Jul 11 2014 - 03:30:02 PDT
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