Hi,
Using workflow tool FEW to generate coordinates files for ligand-receptor
simulation, all the files are generated except the *.lib file. Would you
please help me in this regard. The command I used is as follows:
$AMBERHOME/AmberTools/src/FEW/FEW.pl MMPBSA
/media/Backup/alizadeh/s1p1/FEW/tutorial/tutorial/command_files/commonMDsetup/leap_am1
The massage I qot is as follows:
[ali.localhost ~]$ $AMBERHOME/AmberTools/src/FEW/FEW.pl MMPBSA
/media/Backup/ali
zadeh/s1p1/FEW1/tutorial/cfiles/leap_am1 &
[1] 6688
[ali.localhost ~]$
#####################################################
# #
# FEW #
# Free Energy Workflow #
# #
#####################################################
Checking input parameters and files.
WARNING:
The residue name in the ligand file
/media/Backup/alizadeh/s1p1/FEW1/tutorial/structs/L51g.mol2
you provided is longer than three characters and will be shortened
to the first three characters.
Calculating AM1-BCC charges for ligand L51g.
Generating structures for L51g.
WARNING:
The existing receptor file
/media/Backup/alizadeh/s1p1/FEW1/tutorial/leap/L51g/L51g_rec.pdb
will be re-named to
/media/Backup/alizadeh/s1p1/FEW1/tutorial/leap/L51g/L51g_rec.pdb.setup1.
If you want to use this file for simulation setup later,
please re-change the name into
/media/Backup/alizadeh/s1p1/FEW1/tutorial/leap/L51g/L51g_rec.pdb.
WARNING:
The existing ligand file
/media/Backup/alizadeh/s1p1/FEW1/tutorial/leap/L51g/L51g_lig.pdb
will be re-named to
/media/Backup/alizadeh/s1p1/FEW1/tutorial/leap/L51g/L51g_lig.pdb.setup1.
If you want to use this file for simulation setup later,
please re-change the name into
/media/Backup/alizadeh/s1p1/FEW1/tutorial/leap/L51g/L51g_lig.pdb.
WARNING:
The existing complex file
/media/Backup/alizadeh/s1p1/FEW1/tutorial/leap/L51g/L51g_com.pdb
will be re-named to
/media/Backup/alizadeh/s1p1/FEW1/tutorial/leap/L51g/L51g_com.pdb.setup1.
If you want to use this file for simulation setup later,
please re-change the name into
/media/Backup/alizadeh/s1p1/FEW1/tutorial/leap/L51g/L51g_com.pdb.
Running LEaP for lib-file generation for L51g.
Terminated without warnings.
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Received on Thu May 02 2019 - 03:00:01 PDT
