So I need to run a number of calculations on 200 Lig/proteins so am trying
to write a script to automate the process a little more
I have two input files
*tleap -f leaprc.gaff -f leaprc.ff14SB -f tleap2.txt *
which then opens the file tleap2.txt
*gaff=loadamberparams gaff.datLIG=loadmol2 ./2XHXL.mol2loadamberparams
./2XHXL.frcmodsaveoff LIG 2XHXL.libloadoff ./2XHXL.libcomplex=loadpdb
./2XHX.pdbsolvatebox complex TIP3PBOX 8.0loadamberparams
frcmod.ionsjc_tip3paddIons2 complex Na+ 0addIons2 complex Cl-
0saveamberparm complex 2XHX.prmtop 2XHX.crdquit*
I get this output/error message
-I: Adding /apps_shared/amber/amber14/dat/leap/prep to search path.
-I: Adding /apps_shared/amber/amber14/dat/leap/lib to search path.
-I: Adding /apps_shared/amber/amber14/dat/leap/parm to search path.
-I: Adding /apps_shared/amber/amber14/dat/leap/cmd to search path.
-f: Source leaprc.gaff.
-f: Source leaprc.ff14SB.
-f: Source tleap2.txt.
Welcome to LEaP!
(no leaprc in search path)
Sourcing: /apps_shared/amber/amber14/dat/leap/cmd/leaprc.gaff
Log file: ./leap.log
Loading parameters: /apps_shared/amber/amber14/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.7, Nov 2013)
Sourcing: /apps_shared/amber/amber14/dat/leap/cmd/leaprc.ff14SB
Log file: ./leap.log
Loading parameters: /apps_shared/amber/amber14/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading parameters: /apps_shared/amber/amber14/dat/leap/parm/frcmod.ff14SB
Reading force field modification type file (frcmod)
Reading title:
ff14SB protein backbone and sidechain parameters
Loading library: /apps_shared/amber/amber14/dat/leap/lib/amino12.lib
Loading library: /apps_shared/amber/amber14/dat/leap/lib/aminoct12.lib
Loading library: /apps_shared/amber/amber14/dat/leap/lib/aminont12.lib
Loading library: /apps_shared/amber/amber14/dat/leap/lib/nucleic12.lib
Loading library: /apps_shared/amber/amber14/dat/leap/lib/atomic_ions.lib
Loading library: /apps_shared/amber/amber14/dat/leap/lib/solvents.lib
*Sourcing: ./tleap2.txt
: not foundpen file gaff.dat :
not foundpen file 2XHXL.mol2 :
not foundpen file 2XHXL.frcmod *
saveOff: Argument #1 is type String must be of type: [unit parameter_set
list]
usage: saveOff <object>
<filename>
: not foundpen file
2XHXL.lib
Obviously the issue appears to be in the first few lines of the second file
Or something similar (which I have put in bold myself) though I may have
missed something else.
I have tried to put the gaff.dat file in the current directory and
expressing an absolute path to it
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Received on Fri Aug 17 2018 - 04:00:01 PDT
