AMBER Archive (2004)

Subject: Re: AMBER: amber8 tutorial

From: Viktor Hornak (
Date: Sun Apr 04 2004 - 21:03:56 CDT

Dear Sachin,

Try to use WATBOX216 instead of TIP3PBOX (TIP3P water box unit name has
changed between amber7 and amber8). BTW, "list" command in leap lists
all units that are currently available, you can find out more about the
unit using "desc" command...


Patil, Sachin wrote:

> Hi,
> I am running polyA-polyTtutorial for amber8 on my
> redhat9 machines which has amber7 installed on it.
> Everything went fine untill I used following is xleap
> >solvatebox model TIP3PBOX 8.0
> I got the following error message
> solvateBox : Aurgument #2 is type string must be of type : [unit]
> usage :solvateBox <solute> <solvent> <buffter> [iso] [closeness]
> I dont know what this error message means. But it doesnot solvate the
> DNA. And it doesnot save the polyAT_wat.prmtop and polyAT_wat.inpcrd
> files, since they remain empty.
> ** one interesting point is that, i dont have TIP3 files in the
> /amber7/dat/solvents folder.
> If anybody has any idea please help !
> thanks in advance.
> regards
> sachin

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