AMBER Archive (2008)

Subject: RE: AMBER: solvate dna in TIP3PBOX 10.0

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Jul 24 2008 - 07:29:51 CDT

Hi Collins,

 

In AMBER 9 and 10 WATBOX216 has been renamed as TIP3PBOX so you would
specify.

 

solvateoct dna TIP3PBOX 10.0

 

Good luck,

Ross

 

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Collins Nganou
Sent: Thursday, July 24, 2008 2:29 AM
To: amber_at_scripps.edu
Subject: AMBER: solvate dna in TIP3PBOX 10.0

 

Dear Amber,

I want to solvate dna in solvatebox TIP3PBOX 10.0, by:
> solvateOct dna WATBOX216 10
solvateOct: Argument #2 is type String must be of type: [unit]
usage: solvateOct <solute> <solvent> <buffer> [aniso] [closeness]

But this didn't work.

I use the set of parameters parmbsc0, describe in
http://mmb.pcb.ub.es/PARMBSC0/README.txt

Please someone can tell me how to process.

Thanks a lot.

Regards

Collins

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