This is related to the tutorial A24 wherein FEW workflow is illustrated.
I am trying to learn how to do LIE calculations using Amber18.
I have downloaded the input files from the tutorial and unzipped them. So i have a folder named tutorial and it contains the following sub folders:
-bash-4.2$ cd tutorial/
-bash-4.2$
-bash-4.2$ ls
calc_a_1t cfiles input_info leap.log LIE.pl MD_am1 removeLinks_equi_output.sh TI_am1
calc_a_3t copy_TIprod_output.sh leap lie_am1 link_TIequi_output.sh README structs
-bash-4.2$
I have changed all input/output paths in the lie_am1 file inside cfiles folder as instructed.
I have also set the path for FEW.
Then I execute this command:-
bash-4.2$ perl /usr/local/amber/intel/17.0/mvapich2/2.3/18/AmberTools/src/FEW/FEW.pl LIE ~/LINEAR_ENERGY/tutorial/cfiles/lie_am1
It shows the following error
#####################################################
# #
# FEW #
# Free Energy Workflow #
# #
#####################################################
Checking input parameters and files.
WARNING:
The residue name in the ligand file /users/PHS0297/ohu0513/LINEAR_ENERGY/tutorial/structs/L51c.mol2
you provided is longer than three characters and will be shortened
to the first three characters.
WARNING:
The residue name in the ligand file /users/PHS0297/ohu0513/LINEAR_ENERGY/tutorial/structs/L51d.mol2
you provided is longer than three characters and will be shortened
to the first three characters.
WARNING:
The residue name in the ligand file /users/PHS0297/ohu0513/LINEAR_ENERGY/tutorial/structs/L51g.mol2
you provided is longer than three characters and will be shortened
to the first three characters.
Generation of files for LIE calculation for structure L51c
ERROR:
Execution of external program failed. Please consult the log-file
/users/PHS0297/ohu0513/LINEAR_ENERGY/tutorial/lie_am1/L51c/com/topo/leap_tot.log
for more detailed information about the reasons for the program failure. at /usr/local/amber/intel/17.0/mvapich2/2.3/18/AmberTools/src/FEW/libs/global.pm line 384.
-bash-4.2$
I do not understand why the leap error comes in?
When I go to the specified folder, I run tleap on the example protein totIN.pdb it shows no error!
Any help will be deeply appreciated
Debarati
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Received on Thu Jan 17 2019 - 13:00:03 PST
