AMBER Archive (2008)

Subject: AMBER: RE: problems about TMD in your tutorial

From: Ross Walker (
Date: Mon Nov 10 2008 - 02:20:18 CST

Hi Jakcie,


This is one of the situations where knowing who to script, in something like
bash, or perl comes in handy. Since tleap can read from a file you can write
a script that iterates over the creation of this file and running of tleap
and checks how many waters are added and then adjusts the script as
necessary and repeats.


I'm not sure what you mean by the setbox command solving the problem. Sure
you could read in a pdb containing a fixed number of waters and then just
manually set the box size with setbox but you will still need to create this
initial pdb and deal with any steric clashes between the solvent and the


All the best



From: youban []
Sent: Friday, November 07, 2008 2:49 AM
To: Ross Walker
Subject: Re: problems about TMD in your tutorial


Hi Ross:
thanks for your advise in this special event, however, I thought it will be
too time cost in trying to add water box with different buffer distance,
even in some macromolecules with more than 10 thousand waters.
the second one should be a good idea, but anyway, deleting around 1000
thousand waters from the edge of the box also need some time.
therefore, I wonder whether if I set up periodic boundary condition with the
command of "setbox", which can solve this problems.

2008/11/6 Ross Walker <>

Hi Jakcie,

>I tried your suggestion, but another problem occured
>simutanusly. when I use the commond solvateoct to
>solvate the solute with TIP3P water box in the distance
>of 15A, I found out the same structure with different
>conformations was attached with different number of water
>moloecules, do you know how can I start a same water numbers'
>box parameters for both structures.

This is a common problem. The best way around it is probably just to do a
decimal search on the buffer to use for the other structure. E.g. you can
just do:

mol = loadpdb foo1.pdb
mol1 = copy mol
solvateoct mol1 TIP3PBOX 15.0

If this is more than you want then try:

mol2 = copy mol
solvateoct mol2 TIP3PBOX 14.5

then if this was too small you would try:

mol3 = copy mol
solvateoct mol3 TIP3PBOX 14.7

then say

14.75, 14.74, 14.745 etc etc.

until you get the number of waters you want.

The other option is to open the solvated structure and use the erase command
in the edit window of xleap to delete some waters from around the edge of
the box (an NTP run will take care of any small voids you might create).
There may also be a command line option that will do this in both tleap or
xleap but I don't have the manual to hand.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)