AMBER Archive (2009)

Subject: RE: [AMBER] Amber - Leap- SolvateBox help

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu May 14 2009 - 07:28:36 CDT

Hi Shubhra,

> []$ 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]

The buffer is effectively the amount of water you would like added around
your solute. This specifies the distance between any box edge and any atom
of your solute. Making the buffer smaller means less water which will make
your simulation faster but with the associated approximations of using less
water.

A value of 12.0 (angstroms) is probably reasonable unless you expect your
solute to dramatically change shape during the simulation. Typically you
would not need to specify iso or closeness so use:

solvatebox carb TIP5PBOX 12.0

Note a lot of people prefer TIP4PEW over TIP5P.

Good luck,
Ross

/\
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|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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