AMBER Archive (2008)

Subject: RE: AMBER: Amber 8 Equivalent of the Amber 5 - Edit program

From: Ross Walker (
Date: Wed Feb 06 2008 - 18:35:33 CST

Hi Mohd,
I believe that you can use leap's solvate command to do this. Say your new
molecule's unit name was foo. Then you could do:
foo = loadamberprep foo.prepin
mymol = copy foo
solvatebox mymol foo 10.0
to give you a buffer of foo's of size 10 angstroms around your original
molecule. You may need to repeat this a few times, varying the 10.0 to get
the desired number of molecules. You can also use solvateoct if you'd prefer
a truncated octahedral box instead of rectangular box.
Good luck,
|\oss Walker

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From: [] On Behalf Of
Mohd Farid Ismail
Sent: Wednesday, February 06, 2008 14:08
Subject: AMBER: Amber 8 Equivalent of the Amber 5 - Edit program



I want to make a box of a simple molecule. So what I did is create the
molecule in a program called WebView Pro, and save the pdb file. With this
file, I was able to create .prepin file using antechamber, and using the
prepin file I was able to create the topology and coordinate files using
tleap. (All this is done on a Red Hat machine, using Amber 8, on Intel
platform. I am not sure of the compiler version).


After I did this, I want to make copies of the molecule such that there are
100 of such molecule. I was told by a senior that Amber 5 has Edit, that
will create multiple copies of this molecule (create the coordinates and
charges in a pdb file). Is there a similar program that I can use in Amber
8 to do this?


Thank you.

-Mohd Farid Ismail-

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