Hello,
As far as I know, glycam04 contains "only" information for
carbohydrates but nothing about the solvent. If you want to solvate
your system you should load also ff03 (or ff99) to do the 'solvatoct'
command.
Hope this will help you.
Regards
Florent Barbault
On Tue, 17 Feb 2009 14:51:13 -0500
Heath Watts <hwatts.geosc.psu.edu> wrote:
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
-------------------------------------------------
Dr Florent Barbault
Maitre de conferences / Assistant professor
NEW ADDRESS !!!
Universite Paris Diderot
Laboratoire ITODYS
15 rue Jean de Baïf, bâtiment Lavoisier
75013 Paris FRANCE
http://www.itodys.univ-paris7.fr/
tel : (33) 01-57-27-88-50
e-mail : florent.barbault.univ-paris-diderot.fr
-------------------------------------------------
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Received on Wed Feb 18 2009 - 01:22:04 PST
