AMBER Archive (2009)

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

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Fri May 15 2009 - 18:57:00 CDT

On Thu, May 14, 2009, Shubhra Gupta wrote:
>
> 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
                   ^^^^^^^^^^

I don't think there is any such animal as "TIP5PBOX" in the Amber
distribution. If you type "list" in tleap, you can see what is available, but
this is not a standard object.

> solvateBox: Argument #2 is type String must be of type: [unit]

This (poorly worded) message means that tleap could not find a unit named
TIP5PBOX, and so thought it was seing a string.

[Maybe the UGA people have practical suggestions for using TIP5P as a solvent.]

....dac

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