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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Received on Wed Jun 20 2018 - 05:30:03 PDT
