Hi,
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?
Thanks,
Heath
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Received on Wed Feb 18 2009 - 01:21:53 PST
