Dear AMBER users,
When I ran tleap for metalloprotien,
ie plastocyanin, I got the error message.
I would like to know why I could not
generate the output files.
The following is the input I gave and
the output I got from TLEAP
With thanks
Sincerely Dr. C.Karunakaran
[amkumar.mcwsimsofa ~/karan]$ tleap -f leapp.in
-I: Adding /home/amkumar/soft/amber6/dat to search
path.
-I: Adding /home/amkumar/soft/amber6/dat/leap/lib to
search path.
-I: Adding /home/amkumar/soft/amber6/dat/leap/cmd to
search path.
-f: Source leapp.in.
Welcome to LEaP!
Sourcing leaprc:
/home/amkumar/soft/amber6/dat/leap/cmd/leaprc
Log file: ./leap.log
Loading parameters:
/home/amkumar/soft/amber6/dat/parm94.dat
Loading library:
/home/amkumar/soft/amber6/dat/leap/lib/all_nucleic94.lib
Loading library:
/home/amkumar/soft/amber6/dat/leap/lib/all_amino94.lib
Loading library:
/home/amkumar/soft/amber6/dat/leap/lib/all_aminoct94.lib
Loading library:
/home/amkumar/soft/amber6/dat/leap/lib/all_aminont94.lib
Loading library:
/home/amkumar/soft/amber6/dat/leap/lib/ions94.lib
Loading library:
/home/amkumar/soft/amber6/dat/leap/lib/water.lib
Sourcing: ./leapp.in
Loading parameters: ./frcmodp.pcy
Reading force field mod type file (frcmod)
Loading Prep file: ./mem.in
Loading Prep file: ./hic.in
Loading PDB file: ./1plc1.H.pdb
-- residue 37: duplicate ? atoms (total 3)
ATOM NAMES IN EACH RESIDUE MUST BE UNIQUE:
(same-name atoms are reduced to a single atom)
Created a new atom named: ? within residue: .R<HIC 37>
Created a new atom named: CU within residue: .R<HIC
37>
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-CE-SD-*
+--- With Sp3 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-CG-SD-*
+--- With Sp3 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-CG-SD-*
+--- With Sp3 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-CE-SD-*
+--- With Sp3 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-CG-SD-*
+--- With Sp3 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-CG-SD-*
+--- With Sp3 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-CG-SD-*
+--- With Sp3 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-CE-SD-*
+--- With Sp3 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
total atoms in file: 1443
Leap added 4 missing atoms according to residue
templates:
3 H / lone pairs
1 unknown element
The file contained 2 atoms not in residue templates
Checking Unit.
WARNING: There is a bond of 3.727233 angstroms
between:
------- .R<HIC 37>.A<CA 3> and .R<HIC 37>.A<CD2 15>
WARNING: The unperturbed charge of the unit: -7.000000
is not zero.
FATAL: Atom .R<HIC 37>.A<? 19> does not have a type.
FATAL: Atom .R<HIC 37>.A<CU 20> does not have a type.
Failed to generate parameters
Parameter file was not saved.
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Received on Fri Apr 11 2003 - 02:53:01 PDT
