AMBER Archive (2008)

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

From: Ross Walker (
Date: Thu Nov 06 2008 - 13:32:58 CST

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 |

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