AMBER Archive (2004)

Subject: RE: AMBER: amber8 tutorial

From: Ross Walker (
Date: Sun Apr 04 2004 - 21:45:52 CDT

Dear Sachin,
The polyA-polyT tutorial has been updated and is now designed to work with
AMBER 8 which uses TIP3PBOX for a box of TIP3P water. Previous versions of
amber used WATBOX216 for this.
Thus the command:
solvatebox model WATBOX216 8.0
should work.
I'll add a note about this to the tutorial tomorrow.
All the best
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 |
| EMail:- |
| | PGP Key available on request |


From: [] On Behalf Of
Patil, Sachin
Sent: 04 April 2004 17:03
Subject: AMBER: amber8 tutorial

I am running polyA-polyTtutorial for amber8 on my
redhat9 machines which has amber7 installed on it.

Everything went fine untill I used following is xleap

>solvatebox model TIP3PBOX 8.0

I got the following error message

solvateBox : Aurgument #2 is type string must be of type : [unit]
usage :solvateBox <solute> <solvent> <buffter> [iso] [closeness]

I dont know what this error message means. But it doesnot solvate the DNA.
And it doesnot save the polyAT_wat.prmtop and polyAT_wat.inpcrd files, since
they remain empty.

** one interesting point is that, i dont have TIP3 files in the
/amber7/dat/solvents folder.

If anybody has any idea please help !

thanks in advance.


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