AMBER Archive (2004)

Subject: Re: AMBER: xleap problem

From: David A. Case (
Date: Sun May 02 2004 - 16:07:20 CDT

On Sun, May 02, 2004, hj zou wrote:

> I run into a problem when I try to optimize a ligand in water.
> in XLEAP, I used the following commands:
> > source leaprc.gaff
> ----- Source: /userdata/cluo/amber7/amber7/dat/leap/cmd/leaprc.gaff
> ----- Source of /userdata/cluo/amber7/amber7/dat/leap/cmd/leaprc.gaff done
> Log file: ./leap.log
> Loading parameters: /userdata/cluo/amber7/amber7/dat/leap/parm/gaff.dat
> > mod=loadamberparams frcmod
> Loading parameters: ./frcmod
> Reading force field mod type file (frcmod)
> > loadamberprep lig.prep
> Loading Prep file: ./lig.prep

You need to figure what name is given to the residue in the lig.prep file.
The "list" command should help

> > solvatebox MOL WATBOX216 10
> solvateBox: Argument #1 is type String must be of type: [unit]
> usage: solvateBox <solute> <solvent> <buffer> [iso] [closeness]

"MOL" is not the name of a unit that LEaP knows about.

...good luck...dac
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