TIP3PBOX is undefined because you haven't loaded a water model.
Add the following line to beginning of your tleap inputs:
source leaprc.water.tip3p
Then when you run "list" it should show TIP3PBOX as a defined unit.
Hope this helps,
Robin
On Wed, Sep 20, 2017 at 11:07 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> > solvatebox complex TIP3PBOX 10.0
>
> > solvateBox: Argument #2 is type String must be of type: [unit]
>
> Try 'list' in leap to see what the correct name of the water box might be.
>
> Bill
>
>
> On 9/20/17 11:02 AM, Rana Rehan Khalid wrote:
> > I use solvatebox command for applying boundary condition these command i
> > use
> > source leaprc.protein.ff14SB
> > source leaprc.gaff
> > loadamberparam 1DX.frcmod
> > loadoff idx.lib
> > complex = loadpdb hbay.pdb
> > now I want to add these through tleap but gives error
> >
> > solvatebox complex TIP3PBOX 10.0
> > addions complex Na+ 0
> > addions complex Cl- 0
> >
> > this error comes
> >
> > solvateBox: Argument #2 is type String must be of type: [unit]
> > usage: solvateBox <solute> <solvent> <buffer> [iso] [closeness]
> >
> > then i shall go for
> > saveamberparm complex hbay.prmtop hbay.inpcrd
> >
> > kindly help me to correct the code for solvatebox
> >
> > thanks
> >
> >
> > On Wed, Sep 20, 2017 at 9:57 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
> > wrote:
> >
> >> One more thing when I load the prmtop file and then mdcrd file in the
> vmd
> >> it showed nothing.
> >>
> >> Kindly guide whats the problem here thanks
> >>
> >> On Wed, Sep 20, 2017 at 9:46 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
> >> wrote:
> >>
> >>> I have protein that consist of bay ligand. I follow the antechamber
> >>> tutorial for protein ligand. I extract the ligand and reduced it after
> that
> >>> I produced mol2 file of ligand then by using AM1-BCC charge model.
> >>> Then i produced frcmod file my ligand frcmod file have no missing
> >>> parameter for bond angle and dihedral. It have 7 missing parameters for
> >>> improper. I also attached the frcmod file kindly check and guide if it
> is
> >>> right.
> >>>
> >>> Then i use this script for producing prmtop and inpcrd for ligand (non
> >>> standred residue)
> >>>
> >>> then i prepared the prmtop and inpcrd file for protein complex. BUT
> this
> >>> file work for NBT=0, not work for periodic boundary conditions. How I
> can
> >>> make it workable to run periodic boundary simulation because i want to
> >>> compare this simulation with other simulation by employing similar flag
> >>> commands.
> >>>
> >>> Kindly guide
> >>>
> >>> Thanks
> >>>
> >>
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> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Wed Sep 20 2017 - 11:30:03 PDT
