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
Ross
/\
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|\oss Walker
| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 |
| EMail:- ross.rosswalker.co.uk |
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http://www.rosswalker.co.uk/ | PGP Key available on request |
_____
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Patil, Sachin
Sent: 04 April 2004 17:03
To: amber.scripps.edu
Subject: AMBER: amber8 tutorial
Hi,
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.
regards
sachin
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Received on Mon Apr 05 2004 - 04:53:00 PDT
