Thank you so much for guiding me.
Regards
On Wed, Sep 20, 2017 at 11:14 PM, Robin Betz <robin.robinbetz.com> wrote:
> 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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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
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> >
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Received on Wed Sep 20 2017 - 11:30:03 PDT
