AMBER Archive (2009)

Subject: [AMBER] glycam and solvateoct command

From: Heath Watts (
Date: Tue Feb 17 2009 - 13:51:13 CST

I'm trying to use the .glycam04 force field to with a glucose model. I am
unable to get AMBER to generate the prmtop and inpcrd files when I use
Cerius 2 to build the pdb file. So, I had to do the following:

$AMBERHOME/exe/antechamber -i sustiva.pdb -fi pdb -o sustiva.prepin -fo
prepi -c bcc -s 2

$AMBERHOME/exe/parmchk -i sustiva.prepin -f prepi -o sustiva.frcmod

$AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99

source leaprc.gaff

loadamberprep sustiva.prepin

loadamberparams sustiva.frcmod

solvateoct SUS TIP3PBOX 8.0

This generated the 8.0 A octahedral volume of H2O around my model, as I
wanted it to do.

However, if I use (everything else is the same):

$AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.glycam04

instead of:

$AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99

I get the following message when I run the solvateoct command:

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

usage: solvateOct <solute> <solvent> <buffer> [ansio] [closeness]

What could be causing this error that prevents me from solvating my model?

AMBER mailing list