AMBER Archive (2003)

Subject: AMBER

From: chandran karunakaran (ckaru2000_at_yahoo.com)
Date: Sun Apr 20 2003 - 20:13:32 CDT

Dear AMBER users,

  I am a new user. I ran tleap for
my protein containing two metal atoms
in it.

  I got the following error message.
In my protein, there is no bond between
Zn-C, i dont know why it asks.
I would appreciate if anybody give me
some hint for tackling this.

Thanks in advance

Sincerely Dr.C.Karunakaran

 

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: ./leap.in
Loading parameters: ./frcmod.pcy
Reading force field mod type file (frcmod)
Loading Prep file: ./hicu.in
Loading Prep file: ./asz.in
Loading PDB file: ./1spd.h.pdb
Splitting pdb file residue 48 into HIC and HIE
Splitting pdb file residue 63 into HIC and HIE
 2 residues had naming problems.
 Residues split, so res numbers will not correspond to
pdb.
  Added missing heavy atom: .R<HIC 48>.A<CB 5>
  Added missing heavy atom: .R<HIC 48>.A<C 17>
  Added missing heavy atom: .R<HIC 48>.A<CG 8>
  Added missing heavy atom: .R<HIC 48>.A<O 18>
  Added missing heavy atom: .R<HIC 48>.A<ND1 9>
  Added missing heavy atom: .R<HIC 48>.A<CD2 15>
  Added missing heavy atom: .R<HIC 48>.A<CE1 11>
  Added missing heavy atom: .R<HIC 48>.A<NE2 13>
  Added missing heavy atom: .R<HIE 49>.A<CA 3>
  Added missing heavy atom: .R<HIE 49>.A<N 1>
  Added missing heavy atom: .R<HIC 64>.A<CA 3>
  Added missing heavy atom: .R<HIC 64>.A<CB 5>
  Added missing heavy atom: .R<HIC 64>.A<C 17>
  Added missing heavy atom: .R<HIC 64>.A<CG 8>
  Added missing heavy atom: .R<HIC 64>.A<O 18>
  Added missing heavy atom: .R<HIC 64>.A<ND1 9>
  Added missing heavy atom: .R<HIC 64>.A<CD2 15>
  Added missing heavy atom: .R<HIC 64>.A<CE1 11>
  Added missing heavy atom: .R<HIC 64>.A<NE2 13>
  Added missing heavy atom: .R<HIE 65>.A<N 1>
  Added missing heavy atom: .R<HIC 156>.A<N 1>
  Added missing heavy atom: .R<HIC 156>.A<CA 3>
  Added missing heavy atom: .R<HIC 156>.A<CB 5>
  Added missing heavy atom: .R<HIC 156>.A<C 17>
  Added missing heavy atom: .R<HIC 156>.A<CG 8>
  Added missing heavy atom: .R<HIC 156>.A<O 18>
  Added missing heavy atom: .R<HIC 156>.A<ND1 9>
  Added missing heavy atom: .R<HIC 156>.A<CD2 15>
  Added missing heavy atom: .R<HIC 156>.A<CE1 11>
  Added missing heavy atom: .R<HIC 156>.A<NE2 13>
  Added missing heavy atom: .R<ASZ 157>.A<C 11>
  Added missing heavy atom: .R<ASZ 157>.A<CA 3>
  Added missing heavy atom: .R<ASZ 157>.A<O 12>
  Added missing heavy atom: .R<ASZ 157>.A<N 1>
  Added missing heavy atom: .R<ASZ 157>.A<CB 5>
  Added missing heavy atom: .R<ASZ 157>.A<CG 8>
  Added missing heavy atom: .R<ASZ 157>.A<OD1 9>
  Added missing heavy atom: .R<ASZ 157>.A<OD2 10>
  total atoms in file: 2190
  Leap added 67 missing atoms according to residue
templates:
       38 Heavy
       25 H / lone pairs
       4 unknown element
bond: Argument #1 is type String must be of type:
[atom]
usage: bond <atom1> <atom2> [order]
bond: Argument #1 is type String must be of type:
[atom]
usage: bond <atom1> <atom2> [order]
bond: Argument #1 is type String must be of type:
[atom]
usage: bond <atom1> <atom2> [order]
bond: Argument #1 is type String must be of type:
[atom]
usage: bond <atom1> <atom2> [order]
bond: Argument #1 is type String must be of type:
[atom]
usage: bond <atom1> <atom2> [order]
bond: Argument #1 is type String must be of type:
[atom]
usage: bond <atom1> <atom2> [order]
bond: Argument #1 is type String must be of type:
[atom]
usage: bond <atom1> <atom2> [order]
addIons: 1st Ion & target are the same charge:
     can't neutralize.
  Solute vdw bounding box: 48.390 37.633
44.449
  Total bounding box for atom centers: 54.390 43.633
50.449
  Solvent unit box: 18.774 18.774
18.774
  Total vdw box size: 57.635 46.888
53.455 angstroms.
  Volume: 144455.615 A^3
  Total mass 63469.948 amu, Density 0.730 g/cc
  Added 2596 residues.
Checking Unit.
WARNING: There is a bond of 0.353458 angstroms
between:
------- .R<HIC 48>.A<C 17> and .R<HIE 49>.A<N 1>
WARNING: There is a bond of 26.077951 angstroms
between:
------- .R<HIC 156>.A<C 17> and .R<ASZ 157>.A<N 1>
WARNING: There is a bond of 3.248675 angstroms
between:
------- .R<HIC 156>.A<NE2 13> and .R<HIC 156>.A<CD2
15>
WARNING: There is a bond of 28.702998 angstroms
between:
------- .R<HIC 156>.A<ND1 9> and .R<HIC 156>.A<CU 10>
WARNING: The unperturbed charge of the unit: 2.000000
is not zero.

 -- ignoring the warnings.

Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: C - ZN
Could not find bond parameter for: C - ZN
Building angle parameters.
Could not find angle parameter: ZN - C - N
Could not find angle parameter: O - C - ZN
Could not find angle parameter: CT - C - ZN
Could not find angle parameter: O - C - ZN
Could not find angle parameter: CT - C - ZN
Building proper torsion parameters.
Building improper torsion parameters.
old PREP-specified impropers:
 <HIC 46>: -M CA N H
 <HIC 46>: CA +M C O
 <HIC 46>: CE1 CD2 NE2 HE2
 <HIC 46>: CG NE2 CD2 HD2
 <HIC 46>: ND1 NE2 CE1 HE1
 <HIC 46>: ND1 CD2 CG CB
 <HIC 48>: -M CA N H
 <HIC 48>: CA +M C O
 <HIC 48>: CE1 CD2 NE2 HE2
 <HIC 48>: CG NE2 CD2 HD2
 <HIC 48>: ND1 NE2 CE1 HE1
 <HIC 48>: ND1 CD2 CG CB
 <HIC 64>: -M CA N H
 <HIC 64>: CA +M C O
 <HIC 64>: CE1 CD2 NE2 HE2
 <HIC 64>: CG NE2 CD2 HD2
 <HIC 64>: ND1 NE2 CE1 HE1
 <HIC 64>: ND1 CD2 CG CB
 <ASZ 85>: -M CA N H
 <ASZ 85>: CA +M C O
 <ASZ 85>: CB OD1 CG OD2
 <HIC 156>: -M CA N H
 <HIC 156>: CA +M C O
 <HIC 156>: CE1 CD2 NE2 HE2
 <HIC 156>: CG NE2 CD2 HD2
 <HIC 156>: ND1 NE2 CE1 HE1
 <HIC 156>: ND1 CD2 CG CB
 <ASZ 157>: -M CA N H
 <ASZ 157>: CA +M C O
 <ASZ 157>: CB OD1 CG OD2
 total 448 improper torsions applied
 30 improper torsions in old prep form
Building H-Bond parameters.
Parameter file was not saved.

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