tleap is a program that will generate the system from the command line based on an input file containing all the necessary information, written in the same syntax that is used in xleap.
An example tleap script is:
source leaprc.protein.ff14SB
source leaprc.DNA.OL15
source leaprc.gaff
source leaprc.water.tip3p
loadoff ZN2.lib
loadamberparams ZN2.frcmod
loadamberprep NSA.prepi
loadamberparams NSA.frcmod
NSB = loadmol2 NSB.mol2
loadamberparams NSB.mol2
WTP = loadpdb WT_protein_system.pdb
savepdb WTP WT_protein_system_vac.pdb
saveamberparm WTP WT_protein_system_vac.prmtop WT_protein_system_vac.inpcrd
addions WTP K+ 0.0
solvatebox WTP TIP3PBOX 12.0
savepdb WTP WT_protein_system_wat.pdb
saveamberparm WTP WT_protein_system_wat.prmtop WT_protein_system_wat.inpcrd
quit
When running a tleap script, you can specify the input file with the
-f
flag.
$ $AMBERHOME/bin/tleap -f tleap-script.in
tleap prints a lot of information to the Terminal, and you can watch for any
errors.
Of course, you can send this information to an out file,
if you don’t want to watch everything fail before your eyes
(just make sure it didn’t fail before moving on).
The information that is printed is also saved to an appending leap.log
file,
so the log from every attempt at creating your system is saved without
overwriting by default.
$ $AMBERHOME/bin/tleap -f tleap-script.in > tleap-attempt.out
Note: If you experience issues with a
mol2
saying
that the parameters cannot be found, make sure that the argument you loaded
it in using (NSB
above) matches the 3-letter code for the non-standard.