AMBER Archive (2008)

Subject: AMBER: RE: solvating RNA in 8M urea box

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Jun 05 2008 - 19:12:42 CDT

Hi Paul,

 

I am copying this to the AMBER mailing list which is where such questions
should generally be posted. See http://www.ambermd.org for sign up details.

 

I suspect your problem comes from the fact that leaprc.rna.ff98 loads
solvents.lib but this does not include the 8MUREABOX. Hence Leap does not
know what the unit 8MUREABOX is. You can get a list of the current units
loaded into leap by typing list.

 

The solution is to load the library file that defines this box.

 

loadoff 8Mureabox.off

 

Note the actual name of the unit in the file (in $AMBERHOME/dat/leap/lib) is
UREABOX so your solvate command would be:

 

solvateoct rna1 UREABOX 10.0

 

Good luck,

Ross

 

 

From: pdnichol_at_gmail.com [mailto:pdnichol_at_gmail.com] On Behalf Of Paul
Nichol
Sent: Wednesday, June 04, 2008 12:05 PM
To: amber_tutorial_query_at_rosswalker.co.uk
Subject: solvating RNA in 8M urea box

 

Mr. Walker:

My name is Paul Nichol and I am an undergraduate student at St. Olaf College
in Northfield, Minnesota, USA. I am working on a research project, using
AMBER 9, for which I would like to solvate an RNA duplex in a solution
containing urea. However, I have been unable to successfully use the 8M
urea box solvent model. The command lines I use in xleap, modeled according
to the example on page 30 of the AMBER 9 manual, are

source leaprc.rna.ff98
loadAmberParams frcmod.urea
rna1 = loadpdb "nuc.pdb" (nuc.pdb is the pdb file for the RNA generated
in nucgen)
solvateOct rna1 8MUREABOX 10.0

However, I get an error message in LEaP which says that the command must be
of the type solvateOct <solute> <solvent> <buffer> [aniso] [closeness]

Any advice you might be able to give would be appreciated. Thanks in
advance for your time and attention.

Sincerely,

Paul Nichol

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