AMBER Archive (2009)

Subject: [AMBER] Amber - Leap- SolvateBox help

From: Shubhra Gupta (shubhg_at_iiar.res.in)
Date: Thu May 14 2009 - 00:04:16 CDT


Dear Amber Team Members:

I am using Amber10 to do MD simulation of carbohydrates.
In order to do that I run the following commands

[]$ tleap
> WAT = TP5
> loadAmberParams frcmod.tip5p
> carb = loadpdb carbohy.pdb
> solvateBox carb TIP5PBOX 12.0 0.5

When I run solvateBox command it is given me below suggestion,
but I do not know what should I used for <buffer>.

solvateBox: Argument #2 is type String must be of type: [unit]
usage: solvateBox <solute> <solvent> <buffer> [iso] [closeness]

(leaprc.GLYCAM_06 is already set as a leaprc.)

Thanking You,

Sincerely,
Shubhra

-- 
Shubhra Gupta
Information Officer,
Department of Bioinformatics & Structural Biology
Indian Institute of Advanced Research
Koba Village
Gandhinagar 382007 Gujarat
Phone: 91-79-30514154
Email: shubhg_at_iiar.res.in
Home Page: http://www.guptalab.org/shubhg/
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