Re: [AMBER] how do MM_PBSA without water

From: Bill Miller III <>
Date: Sun, 18 Apr 2010 09:18:53 -0400

Simply adding 'intial_traj=1' in the &general namelist of the
input file will take care of this for you.

This isn't much more complicated using either. In the .MAKECRD
section make sure you set 'BOX' as 'NO' and then just fill in the rest of
the information as explained in the AMBER Manual (start frame, end frame,
ligand atom numbers, receptor atom numbers, etc). Note that this section is
only used when generating snapshots (GC) is turned on (i.e. set to 1).

Good luck!


On Sun, Apr 18, 2010 at 3:48 AM, geyan <> wrote:

> Dear Amber users,
> I have got the trajectory of a system of DNA-Protein complex. Because I
> konw they'are interacting with each other without water in nature,so I
> didn't add solvent effect.Now the problem is,how I alter the script from the
> Amber Tutorial of MM_pbsa to extract snapshot and do the accurate PBSA
> analysis.The standard input of the two scripts is a little too complex for
> me to change,it has beyond my scope.
> Any help is appreciated
> 2010-04-18
> geyan
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Received on Sun Apr 18 2010 - 06:30:02 PDT
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