AMBER Archive (2003)

Subject: Metalloprotein

From: chandran karunakaran (ckaru2000_at_yahoo.com)
Date: Mon Apr 14 2003 - 20:18:39 CDT

Dear Amber users,

  Would you kindly advice me how to
overcome this error which I got
when I ran tleap for plastocyanin.

With thanks

Sincerely yours
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: ./leapp.in
Loading parameters: ./frcmodp.pcy
Reading force field mod type file (frcmod)
Loading Prep file: ./mem.in
Loading Prep file: ./hicu.in
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
templates:
       10 Heavy
       7 H / lone pairs
       1 unknown element
Checking Unit.
WARNING: There is a bond of 3.223311 angstroms
between:
------- .R<HIC 37>.A<CU 10> and .R<MET 92>.A<SD 11>
WARNING: There is a bond of 31.183065 angstroms
between:
------- .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.

--- "David A. Case" <case_at_scripps.edu> wrote:
> On Sun, Apr 13, 2003, yuan bo wrote:
>
> > I am simulating protein in mixed solents and saved
> > trajectory in every 0.2ps for analysis. now I want
> to
> > calculate diffusion coefficients of solvent for
> one
> > 100ps trajectory ( 500=100/0.2 sets data, using
> Ptraj
> > program in Amber 6. Manual define diffusion as
> > follows:
> > diffusion mask time_per_frame [ average ] [
> > filenameroot ]
> > The time_per_frame sepicifies time between frams
> in
> > ps. I use " diffusion :WAT 4 average filename"
> command
>
> If the time between your snapshots (frames) is 0.2
> ps, why did you
> put "4" in your command for time_per_frame? I think
> that number should
> be 0.2.
>
> ..hope this helps...dac
>
> --
>
>
==================================================================
> David A. Case | e-mail:
> case_at_scripps.edu
> Dept. of Molecular Biology, TPC15 | fax:
> +1-858-784-8896
> The Scripps Research Institute | phone:
> +1-858-784-9768
> 10550 N. Torrey Pines Rd. | home page:
>
> La Jolla CA 92037 USA |
> http://www.scripps.edu/case
>
==================================================================
>

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