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
> > _______________________________________________
> > AMBER mailing list
> > 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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Received on Wed Jun 20 2018 - 06:30:02 PDT
