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 - 05:30:02 PDT
