From: chandran karunakaran <>
Date: Tue, 15 Apr 2003 16:55:16 -0700 (PDT)

Dear AMBER users,

  I am interested in molecular dynamics of
mutant copper proteins. Before I do that,
I tried with plastocyanin. Thanks for
correcting me to include Cu in HIC
residue. Afterwards I ran and got this
output. Could any one suggest me what
should I do? Sorry for disturbance.
  With thanks

  Sincerely yours

Welcome to LEaP!
Sourcing leaprc:
Log file: ./leap.log
Loading parameters:
Loading library:
Loading library:
Loading library:
Loading library:
Loading library:
Loading library:
Sourcing: ./
Loading parameters: ./frcmodp.pcy
Reading force field mod type file (frcmod)
Loading Prep file: ./
Loading Prep file: ./
Loading PDB file: ./1plc.H.pdb
  Added missing heavy atom: .R<HIC 100>.A<N 1>
  Added missing heavy atom: .R<HIC 100>.A<CA 3>
  Added missing heavy atom: .R<HIC 100>.A<CB 5>
  Added missing heavy atom: .R<HIC 100>.A<C 17>
  Added missing heavy atom: .R<HIC 100>.A<CG 8>
  Added missing heavy atom: .R<HIC 100>.A<O 18>
  Added missing heavy atom: .R<HIC 100>.A<ND1 9>
  Added missing heavy atom: .R<HIC 100>.A<CD2 15>
  Added missing heavy atom: .R<HIC 100>.A<CE1 11>
  Added missing heavy atom: .R<HIC 100>.A<NE2 13>
  total atoms in file: 1442
  Leap added 18 missing atoms according to residue
       10 Heavy
       7 H / lone pairs
       1 unknown element
Checking Unit.
WARNING: There is a bond of 3.223311 angstroms
------- .R<HIC 37>.A<CU 10> and .R<MET 92>.A<SD 11>
WARNING: There is a bond of 31.183065 angstroms
------- .R<HIC 100>.A<ND1 9> and .R<HIC 100>.A<CU 10>
WARNING: The unperturbed charge of the unit: -6.000000
is not zero.

 -- ignoring the warnings.

Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Could not find angle parameter: S - CU - S
Building proper torsion parameters.
Building improper torsion parameters.
old PREP-specified impropers:
 <HIC 37>: -M CA N H
 <HIC 37>: CA +M C O
 <HIC 37>: CE1 CD2 NE2 HE2
 <HIC 37>: CG NE2 CD2 HD2
 <HIC 37>: ND1 NE2 CE1 HE1
 <HIC 37>: ND1 CD2 CG CB
 <HIC 100>: -M CA N H
 <HIC 100>: CA +M C O
 <HIC 100>: CE1 CD2 NE2 HE2
 <HIC 100>: CG NE2 CD2 HD2
 <HIC 100>: ND1 NE2 CE1 HE1
 <HIC 100>: ND1 CD2 CG CB
 total 293 improper torsions applied
 12 improper torsions in old prep form
Building H-Bond parameters.
Parameter file was not saved.

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Received on Wed Apr 16 2003 - 01:53:01 PDT
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