Re: AMBER: Problem with setbox command...

From: David A. Case <>
Date: Thu, 30 Mar 2006 08:06:04 -0800

On Thu, Mar 30, 2006, Ilyas Yildirim wrote:
> I have created a structure using nucgen (test.pdb). Then I used the
> following script ( in xleap to create the prmtop and inpcrd
> files:
> ---------------------- --------------------------
> molecule = loadpdb test.pdb
> solvateoct molecule TIP3PBOX 8.0
> savepdb molecule test_xleap.pdb
> saveamberparm molecule prmtop_01 inpcrd_01
> quit
> -------------------------------------------------------------
> Then, I have used the following script on the solvated structure created
> in the above script (test_xleap.pdb).
> ---------------------- --------------------------
> source leaprc.rna.ff99
> molecule = loadpdb test_xleap.pdb
> setbox molecule centers
> saveamberparm molecule prmtop_02 inpcrd_02
> -------------------------------------------------------------
> In this second case I am using the setbox command to create the box
> information in the prmtop_02 file.

The problem is that "setbox" is for a rectangular system (which might be
created, for example, by "solvatebox". You are trying to use it on a system
created with "solvateoct", and that won't work. If you use "solvatebox"
in your 01 example, you should have a shot a making this work.

> PS: I was thinking to copy/paste the box info of the first inpcrd_01
> 38.6491104 38.6491104 38.6491104 109.4712190 109.4712190 109.4712190
> to the second inpcrd_02.

This is worth a try (i.e. it should work, but test carefully!). Another
option is use just the solute for the second case, and use trial and error
with distance parameter in solvateoct to get the desired number of water

> Also I was thinking to change the box info in
> the prmtop_02 file with the prmtop_01 box info.
> 9.00000000E+01 3.76940000E+01 4.33120000E+01 4.27090000E+01

This will do no good: the box information in the prmtop file is no longer
used -- those values are just placeholders for backwards compatibiltiy with
older versions of Amber. The last line of the inpcrd file contains the
"real" information.

....good luck...dac

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Apr 02 2006 - 06:10:13 PDT
Custom Search