AMBER Archive (2008)

Subject: Re: AMBER: 3fe-4s cluster parameter file generation

From: moitrayee_at_mbu.iisc.ernet.in
Date: Tue Sep 16 2008 - 13:01:59 CDT

I have done the prescribed modifications, but when i do saveamberparm i get the
following error message:

Welcome to LEaP!
Sourcing leaprc: ./leaprc
----- Source: /soft/amber8/dat/leap/cmd/leaprc.gaff
----- Source of /soft/amber8/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /soft/amber8/dat/leap/parm/gaff.dat
----- Source: /soft/amber8/dat/leap/cmd/leaprc.ff03
----- Source of /soft/amber8/dat/leap/cmd/leaprc.ff03 done
Log file: ./leap.log
Loading parameters: /soft/amber8/dat/leap/parm/parm99.dat
Loading parameters: /soft/amber8/dat/leap/parm/frcmod.ff03
Reading force field mod type file (frcmod)
Loading library: /soft/amber8/dat/leap/lib/all_amino03.lib
Loading library: ./ions94.lib
Loading library: /soft/amber8/dat/leap/lib/solvents.lib
Loading library: /soft/amber8/dat/leap/lib/all_nucleic94.lib
Loading library: /soft/amber8/dat/leap/lib/all_aminoct94.lib
Loading library: /soft/amber8/dat/leap/lib/all_aminont94.lib
Sourcing: ./teleap.in
Loading parameters: ./F3S.frcmod
Reading force field mod type file (frcmod)
Loading Prep file: ./F3S.in
Loading PDB file: ./1EA0_A.pdb
  Added missing heavy atom: .R<CLEU 1452>.A<OXT 20>
  total atoms in file: 11187
  Leap added 11217 missing atoms according to residue templates:
       1 Heavy
       11216 H / lone pairs
addIons: Argument #2 is type String must be of type: [unit]

    addIons unit ion1 #ion1 [ion2 #ion2]

        UNIT _unit_
        UNIT _ion1_
        NUMBER _#ion1_
        UNIT _ion2_
        NUMBER _#ion2_

Adds counterions in a shell around _unit_ using a Coulombic potential
on a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be
opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise,
the specified numbers of _ion1_ [_ion2_] are added [in alternating order].
If solvent is present, it is ignored in the charge and steric calculations,
and if an ion has a steric conflict with a solvent molecule, the ion is
moved to the center of said molecule, and the latter is deleted. (To
avoid this behavior, either solvate _after_ addions, or use addIons2.)
Ions must be monoatomic. Note that the one-at-a-time procedure is not
guaranteed to globally minimize the electrostatic energy. When neutralizing
regular-backbone nucleic acids, the first cations will generally be added
between phosphates, leaving the final two ions to be placed somewhere around
the middle of the molecule.
The default grid resolution is 1 Angstrom, extending from an inner radius
of (max ion size + max solute atom size) to an outer radius 4 Angstroms
beyond. A distance-dependent dielectric is used for speed.

 (using default radius 1.500000 for FE3)
 (using default radius 1.500000 for FE2)
 (using default radius 1.500000 for FE1)
  Solute vdw bounding box: 99.030 95.185 96.959
  Total bounding box for atom centers: 119.030 115.185 116.959
  Solvent unit box: 18.774 18.774 18.774
 (using default radius 1.500000 for FE3)
 (using default radius 1.500000 for FE2)
 (using default radius 1.500000 for FE1)
  Total vdw box size: 121.840 118.521 119.755 angstroms.
  Volume: 1729331.050 A^3
  Total mass 935216.842 amu, Density 0.898 g/cc
  Added 43069 residues.
Checking Unit.
WARNING: There is a bond of 7.224966 angstroms between:
------- .R<THR 304>.A<C 13> and .R<THR 305>.A<N 1>
WARNING: There is a bond of 10.331638 angstroms between:
------- .R<VAL 1168>.A<C 15> and .R<ASP 1169>.A<N 1>
WARNING: There is a bond of 25.906360 angstroms between:
------- .R<GLY 1182>.A<C 6> and .R<GLY 1183>.A<N 1>
WARNING: There is a bond of 3.265214 angstroms between:
------- .R<F3S 1453>.A<S3 3> and .R<F3S 1453>.A<S4 4>
WARNING: There is a bond of 3.432639 angstroms between:
------- .R<F3S 1453>.A<S2 2> and .R<F3S 1453>.A<S3 3>
WARNING: The unperturbed charge of the unit: -8.000010 is not zero.

 -- ignoring the warnings.

Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: FE - FE
Could not find bond parameter for: FE - FE
Could not find bond parameter for: S - FE
Building angle parameters.
Could not find angle parameter: FE - FE - FE
Could not find angle parameter: S - S - FE
Could not find angle parameter: S - FE - FE
Could not find angle parameter: S - S - S
Could not find angle parameter: S - S - FE
Could not find angle parameter: S - S - S
Building proper torsion parameters.
 ** No torsion terms for S-S-FE-FE
 ** No torsion terms for S-FE-FE-FE
 ** No torsion terms for S-S-FE-FE
 ** No torsion terms for S-S-S-S
 ** No torsion terms for S-S-S-FE
Building improper torsion parameters.
old PREP-specified impropers:
 total 4411 improper torsions applied
 0 improper torsions in old prep form
Building H-Bond parameters.
Parameter file was not saved.
        Quit
Please suggest what should i do? Thank you a lot.

Sincere Regards
Moitrayee

>> I am attaching the structure of my ligand. In that case is my prepc file
>> connectivities alright.
>
> No - look closely at the examples in
>
>> http://amber.scripps.edu/doc/prep.html
>
> I think what you want is (starting at top left and going clockwise)
>
> S M
> Fe M
> S E
> S M
> Fe M
> S M
> Fe M
>
> LOOP
> <1st S to last Fe>
>
> Bill
> ----------------------------------------------------------------------- 

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