Re: [AMBER] create a prmtop file without water & ions,

From: Jason Swails <>
Date: Fri, 2 Jul 2010 01:46:17 -0400

Hi Homa,

This is a general tip for all would-be MM/PBSA users, whether you're using
the perl and/or python script: Create all of your topology files at the
same time with the same leap script. Typically, you create the complex by
using the "combine" keyword. You can use saveamberparm for the receptor and
ligand before you combine them, and again for the complex before you solvate
and add ions. See the section for preparing for MM/PBSA calculations in the section of the Amber11 manual. It's available on
The standalone copy of the manual, found on , also has
this section.

That being said, the above is also useful if you want to simply save only
solute coordinates (with ntwprt) or strip the water and ions afterwards and
visualize only the protein. You can create the dry topology files with any
leap program: tleap, xleap, or sleap. The starting PDB file will also do
fine. Keep in mind that the topology file just has the bond connectivity
and other parameters, no coordinates. Thus, as long as it matches up with
the coordinates stripped of waters and ions, then it should work.

Hope this helps,

On Thu, Jul 1, 2010 at 11:13 PM, Homa Azizian <>wrote:

> Hi amber users,
> I want to know how could I create a prmtop file without water & ions, for
> the trajectories that stript the water.
> Is it correct to do it from the xleap. with the starting pdb that used to
> produced the topology with water?
> Thanks for replying
> Homa
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Thu Jul 01 2010 - 23:00:03 PDT
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