Hi Gamze,
The link I sent has the updated tutorial files.
You will need to
1) download the zipped file with the new tutorial
2) Extract it and put it in a separate folder
3) Open index.htm with a web browser of your choice.
Best,
Tom
On Thu, Jun 21, 2018 at 5:31 AM, Gamze Özbay <gamze.ozbayyy.gmail.com>
wrote:
> Hi Tom,
> I am sorry but i didnt understand how to use the files. If there is a
> tutorial that includes the codes like in this website:
> http://ambermd.org/tutorials/advanced/tutorial25/section1.htm could you
> please send it to me? The codes in here does not work on tleap.
>
> Best,
>
> Gamze
>
> 2018-06-20 16:28 GMT+03:00 Tom Kurtzman <simpleliquid.gmail.com>:
>
> > Hi Gamze,
> >
> > We recently updated the GIST tutorial and are in the process of updating
> > the website. The new files are here:
> >
> > https://www.dropbox.com/sh/6zr7y0modgeaxq6/
> AACb0CQi5XkdkUyAV65ijakza?dl=0
> >
> > Best,
> >
> > Tom
> >
> > On Wed, Jun 20, 2018 at 8:25 AM, Daniel Roe <daniel.r.roe.gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > The error message is clear: you are trying to load a file that does not
> > > exist.
> > >
> > > That being said, the tutorial looks like it might need an overhaul. It
> > > does mention a PDB at the outset (1FJS.pdb) but then the example input
> > > immediately following uses 'ChainA_IONS_H.pdb' instead. Try replacing
> > > ChainA_IONS_H.pdb with 1FJS.pdb.
> > >
> > > Hope this helps,
> > >
> > > -Dan
> > >
> > > On Wed, Jun 20, 2018 at 8:19 AM, Gamze Özbay <gamze.ozbayyy.gmail.com>
> > > wrote:
> > > > Hi all, i am using ambert18 and tryiing GIST tutorial at
> > > > http://ambermd.org/tutorials/advanced/tutorial25/section1.htm While
> > > using
> > > > tleap, i entered those commands and had these errors :
> > > >> source leaprc.protein.ff14SB
> > > > ----- Source: /home/gamze/amber18/dat/leap/cmd/leaprc.protein.ff14SB
> > > > ----- Source of /home/gamze/amber18/dat/leap/
> cmd/leaprc.protein.ff14SB
> > > done
> > > > Log file: ./leap.log
> > > > Loading parameters: /home/gamze/amber18/dat/leap/parm/parm10.dat
> > > > Reading title:
> > > > PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
> > > > Loading parameters: /home/gamze/amber18/dat/leap/parm/frcmod.ff14SB
> > > > Reading force field modification type file (frcmod)
> > > > Reading title:
> > > > ff14SB protein backbone and sidechain parameters
> > > > Loading library: /home/gamze/amber18/dat/leap/lib/amino12.lib
> > > > Loading library: /home/gamze/amber18/dat/leap/lib/aminoct12.lib
> > > > Loading library: /home/gamze/amber18/dat/leap/lib/aminont12.lib
> > > >> loadamberparams frcmod.ff14SB
> > > > Loading parameters: /home/gamze/amber18/dat/leap/parm/frcmod.ff14SB
> > > > Reading force field modification type file (frcmod)
> > > > Reading title:
> > > > ff14SB protein backbone and sidechain parameters
> > > >> prot = loadpdb ChainA_IONS_H.pdb
> > > >
> > > > Error: Could not open file ChainA_IONS_H.pdb: not found
> > > >> solvateBox prot TIP3PBOX 10
> > > >
> > > > Error: solvateBox: Argument #1 is type String must be of type: [unit]
> > > > usage: solvateBox <solute> <solvent> <buffer> [iso] [closeness]
> > > >> loadoff Ca2.lib
> > > >
> > > > Error: Could not open file Ca2.lib: not found
> > > >
> > > > Error: Could not open database: Ca2.lib
> > > >> quit
> > > > Quit
> > > > I couldnt solve the problem. Please help. Thanks,
> > > >
> > > > Gamze Ozbay
> > > > _______________________________________________
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> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > ************************************************
> > Tom Kurtzman, Ph.D.
> > Associate Professor
> > Department of Chemistry
> > Lehman College, CUNY
> > 250 Bedford Park Blvd. West
> > Bronx, New York 10468
> > 718-960-8832
> > http://www.lehman.edu/faculty/tkurtzman/
> > <http://www.lehman.edu/faculty/tkurtzman/index.html>
> > ************************************************
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> >
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************************************************
Tom Kurtzman, Ph.D.
Associate Professor
Department of Chemistry
Lehman College, CUNY
250 Bedford Park Blvd. West
Bronx, New York 10468
718-960-8832
http://www.lehman.edu/faculty/tkurtzman/
<http://www.lehman.edu/faculty/tkurtzman/index.html>
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Received on Thu Jun 21 2018 - 09:30:02 PDT
