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
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > 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 Thu Jun 21 2018 - 03:00:02 PDT
