Dear Karunakaran:
In AMBER (and virtually all other MM force fields), parameters are
associated with atom types. From the message below, it is suggested that
you did not input the atom types for atoms 19 and 20 of your HIC. You
can first use leap to edit HIC (xleap would do a good job on this) to
give atom types. After that, you also need to figure out parameters for
these atoms which include bond, bond angles, dihedrals, charges, and van
der Waals parameters.
Good luck!
yong
-----Original Message-----
From: chandran karunakaran [mailto:ckaru2000.yahoo.com]
Sent: Thursday, April 10, 2003 9:21 PM
To: amber.heimdal.compchem.ucsf.edu
Subject: Re: Tleap-metalloprotein
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 - 03:53:01 PDT
