Dear David A Case
thanks for your suggestion and help. I tried the manual again and I realize
that the problem is the xleap. it's a bite difficult to draw molecules with
it. I draw the molecules correctly and run next commands. at the tleap
commands sth appeared about unit and ... . I saw the manual and mailing
list but I couldn't find useful suggestion. What should I do at this step?
unit? files?
thanks in advanced
nasiri
$ tleap -f commands.in
-I: Adding /home/nasiri/amber12//dat/leap/prep to search path.
-I: Adding /home/nasiri/amber12//dat/leap/lib to search path.
-I: Adding /home/nasiri/amber12//dat/leap/parm to search path.
-I: Adding /home/nasiri/amber12//dat/leap/cmd to search path.
-f: Source commands.in.
Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./commands.in
----- Source: /home/nasiri/amber12//dat/leap/cmd/leaprc.gaff
----- Source of /home/nasiri/amber12//dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /home/nasiri/amber12//dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.5, January 2013)
Loading Mol2 file: ./bmi.mol2
Reading MOLECULE named bmi
Loading Mol2 file: ./bf4.mol2
Reading MOLECULE named bf4
Loading Mol2 file: ./acn.mol2
Reading MOLECULE named acn
Could not open file ionicbox.pdb: not found
Loading parameters: ./frcmod.bf4
Reading force field modification type file (frcmod)
Reading title:
remark goes here
Loading parameters: ./frcmod.bmi
Reading force field modification type file (frcmod)
Reading title:
remark goes here
Loading parameters: ./frcmod.acn
Reading force field modification type file (frcmod)
Reading title:
remark goes here
setBox: Argument #1 is type String must be of type: [unit]
usage: setBox <unit> vdw|centers [ clearance | <clearance_xyz_list> ]
saveAmberParm: Argument #1 is type String must be of type: [unit]
usage: saveAmberParm <unit> <topologyfile> <coordfile>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Nov 23 2013 - 03:00:02 PST
