Re: [AMBER] adding/deleting water molecules in leap

From: Jason Swails <>
Date: Thu, 3 May 2012 21:15:23 -0400

On Thu, May 3, 2012 at 6:59 PM, Jason Swails <> wrote:

> You can delete extra atom molecules from your topology file using
> or cpptraj from AmberTools 12

I will elaborate here to tell you exactly how to do this using ParmEd. You
have to download AmberTools 12 to access this program (which is available
as a free download from Then, tweak your box size to get as
close as possible to the number of water molecules that you want, but make
SURE that LEaP gives you *more* water molecules than you desire, since
ParmEd (and cpptraj) can only strip atoms from the topology file -- not add

After you do this, you should have a topology file and a inpcrd file, I'll
call them "prmtop" and "inpcrd" for this example. For this example, I will
also assume you want to get rid of 12 water molecules (which is 12
different residues).

First open up your prmtop file in ( prmtop). The
commands you will want to use are the following:

loadRestrt inpcrd
strip :5015-5026
outparm prmtop2 inpcrd2

The first command will load your inpcrd file in as the coordinates. The
second command deletes the 12 (yes, 12) residues 5015 -- 5026 (the numbers
will change based on your real prmtop -- you can use the command
"printPointers" to print the value of "NRES" -- that will tell you how many
residues you have total so you can figure out which ones you want to
delete). The last command will print out the new topology file "prmtop2"
and the corresponding coordinate file "inpcrd2" with your desired number of
water molecules.

Some caveats: After stripping the topology file, ParmEd reconstructs the
topology file, which means that it may internally reorder some pointers,
but the actual parameters will be the same. ParmEd does *not* recalculate
the box dimensions -- it keeps the original. Keep this in mind if you
delete a *lot* of water molecules. (the GUI version) does not
yet give you the option of saving a coordinate file, so you have to use the
text-based version ( This should work perfectly fine if you
just want to delete a handful of waters, though.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Thu May 03 2012 - 18:30:04 PDT
Custom Search