You're right. Something weird happens with tleap in Ambert16.
I've tried with AT15 and works fine but got similar error with 16 version.
Hai
On Thu, Jul 7, 2016 at 11:13 AM, Corum, Katharine W <
katharine-corum.uiowa.edu> wrote:
>
> Hi,
>
>
> I am using this tutorial from the website:
> http://ambermd.org/tutorials/advanced/tutorial2/section1.htm
>
>
> I attached the pdb file that goes with the tutorial. I do not have an
> output file yet as I have not reached that point. I just have an error with
> my commands.
>
>
> According to the tutorial in order solvate the box the command takes 3
> mandatory arguments and 1 optional argument in the form of:
>
>
> solvatebox solute solvent buffer ["iso"] [closeness]
>
>
> This tutorial uses a box of TIP3P water so my command is:
>
>
> solvatebox NMA TIP3PBOX 15
>
>
> However, when I type this in I get a message of:
>
>
> > solvatebox NMA TIP3PBOX 15
>
> solvateBox: Argument #2 is type String must be of type: [unit]
>
> usage: solvateBox <solute> <solvent> <buffer> [iso] [closeness]
>
>
> Thanks for the help!
>
> Amber Tutorials - A2 Section 1<
> http://ambermd.org/tutorials/advanced/tutorial2/section1.htm>
> ambermd.org
> A tutorial on running coupled potential Quantum Mechanics / Molecular
> Mechanics (QM/MM) simulation s using AMBER - Section 1
>
>
>
> ________________________________
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Sent: Thursday, July 7, 2016 10:03:53 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Amber16 tutorials
>
> Hi,
>
> It would be better if you posted your entire leap input and output -
> otherwise we have to guess at what is going wrong.
>
> -Dan
>
> On Thu, Jul 7, 2016 at 8:54 AM, Corum, Katharine W
> <katharine-corum.uiowa.edu> wrote:
> > Hi,
> >
> >
> > I used this command...
> >
> >
> > NMA = loadpdb NMA_skeleton.pdb
> >
> > ________________________________
> > From: Hirdesh Kumar <hirdesh.iitd.gmail.com>
> > Sent: Thursday, July 7, 2016 9:52:20 AM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] Amber16 tutorials
> >
> > how did you load your protein??
> > NMA = loadpdb xyz.pdb
> >
> > Is it NMA? or some other variable?
> >
> > *?*
> >
> > On Thu, Jul 7, 2016 at 4:43 PM, Corum, Katharine W <
> > katharine-corum.uiowa.edu> wrote:
> >
> >> Hi, I am stuck on this tutorial again. The command solvatebox NMA
> TIP3PBOX
> >> 15 does not work. The terminal says...
> >>
> >>
> >> > solvatebox NMA TIP3PBOX 15
> >>
> >> solvateBox: Argument #2 is type String must be of type: [unit]
> >>
> >> usage: solvateBox <solute> <solvent> <buffer> [iso] [closeness]
> >>
> >>
> >> Thanks!
> >>
> >>
> >> ________________________________
> >> From: Corum, Katharine W
> >> Sent: Wednesday, July 6, 2016 4:16:06 PM
> >> To: AMBER Mailing List
> >> Subject: Re: [AMBER] Amber16 tutorials
> >>
> >>
> >> Thank you!
> >>
> >> ________________________________
> >> From: Hai Nguyen <nhai.qn.gmail.com>
> >> Sent: Wednesday, July 6, 2016 4:14:49 PM
> >> To: AMBER Mailing List
> >> Subject: Re: [AMBER] Amber16 tutorials
> >>
> >> hi,
> >>
> >> You need to download NMA_skeleton.pdb to your computer. There is a link
> in
> >> the webpage:
> http://ambermd.org/tutorials/advanced/tutorial2/section1.htm
> >>
> >> Also, in that page, change
> >>
> >> $AMBERHOME/bin/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff14SB
> >>
> >> to
> >>
> >> $AMBERHOME/bin/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.protein.ff14SB
> >>
> >> Hai
> >>
> >> On Wed, Jul 6, 2016 at 5:07 PM, Corum, Katharine W <
> >> katharine-corum.uiowa.edu> wrote:
> >>
> >> > Hi! I am new to Amber. I have just installed Amber16. Are there any
> >> > tutorials that work for Amber16? I have been trying to do tutorials
> but
> >> > keep getting stuck since they are only updated for Amber15. I am
> >> interested
> >> > in all tutorials, especially QM/MM ones.
> >> >
> >> >
> >> > I would love to do this tutorial but I keep getting a message saying
> >> there
> >> > is no NMA_skeleton.pdb file. Any help would be greatly appreciated!
> >> >
> >> >
> >> > Thanks!
> >> >
> >> > Katie
> >> >
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
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> >> AMBER.ambermd.org
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> >>
> > _______________________________________________
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> > AMBER.ambermd.org
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>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
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Received on Thu Jul 07 2016 - 08:30:05 PDT
