Re: [AMBER] Amber16 tutorials

From: Hirdesh Kumar <hirdesh.iitd.gmail.com>
Date: Thu, 7 Jul 2016 16:52:20 +0200

how did you load your protein??
NMA = loadpdb xyz.pdb

Is it NMA? or some other variable?

*‚Äč*

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
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Thu Jul 07 2016 - 08:00:03 PDT
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