AMBER Archive (2009)

Subject: [AMBER] Problem with nonstandard residues

From: moitrayee_at_mbu.iisc.ernet.in
Date: Tue May 19 2009 - 06:48:33 CDT

Dear Amber Users,

I am trunig to build the prmtop and prmcrd files for my system. I have obtained
the respective prepi and frcmod files required for the non-standard residues in
the pdb. Including them in my script for leap as given below:
loadAmberParams TSB.frcmod
loadAmberPrep TSB.in
2qf6 = loadpdb 1QF6_TSB.pdb
addions 2qf6 Na+ 0
solvatebox 2qf6 TIP3PBOX 10.00 0.75
saveamberparm 2qf6 2qf6.prmtop 2qf6.prmcrd
quit
I get the following error:

-I: Adding /soft/amber8/dat/leap/prep to search path.
-I: Adding /soft/amber8/dat/leap/lib to search path.
-I: Adding /soft/amber8/dat/leap/parm to search path.
-I: Adding /soft/amber8/dat/leap/cmd to search path.
-f: Source teleap.in.

Welcome to LEaP!
Sourcing leaprc: ./leaprc
----- 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
----- 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
Sourcing: ./teleap.in
----- 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
Loading parameters: ./TSB.frcmod
Reading force field mod type file (frcmod)
Loading Prep file: ./TSB.in
Loading PDB file: ./1QF6_TSB.pdb
  Added missing heavy atom: .R<TSB 644>.A<O3 16>
  Added missing heavy atom: .R<TSB 644>.A<P1 17>
  Added missing heavy atom: .R<TSB 644>.A<O6 18>
  Added missing heavy atom: .R<TSB 644>.A<O7 19>
  Added missing heavy atom: .R<TSB 644>.A<O2 20>
  Added missing heavy atom: .R<TSB 644>.A<C10 21>
  Added missing heavy atom: .R<TSB 644>.A<C7 24>
  Added missing heavy atom: .R<TSB 644>.A<C8 25>
  Added missing heavy atom: .R<TSB 644>.A<O1 34>
  Added missing heavy atom: .R<TSB 644>.A<C9 26>
  Added missing heavy atom: .R<TSB 644>.A<O4 30>
  Added missing heavy atom: .R<TSB 644>.A<C6 35>
  Added missing heavy atom: .R<TSB 644>.A<O5 27>
  Added missing heavy atom: .R<TSB 644>.A<N1 37>
  Added missing heavy atom: .R<TSB 644>.A<C2 38>
  Added missing heavy atom: .R<TSB 644>.A<C1 41>
  Added missing heavy atom: .R<TSB 644>.A<N2 39>
  Added missing heavy atom: .R<TSB 644>.A<C3 42>
  Added missing heavy atom: .R<TSB 644>.A<N3 50>
  Added missing heavy atom: .R<TSB 644>.A<C5 43>
  Added missing heavy atom: .R<TSB 644>.A<C4 48>
  Added missing heavy atom: .R<TSB 644>.A<N5 44>
  Added missing heavy atom: .R<TSB 644>.A<N4 47>
  Added missing heavy atom: .R<TSB 645>.A<C11 14>
  Added missing heavy atom: .R<TSB 645>.A<C12 9>
  Added missing heavy atom: .R<TSB 645>.A<O8 15>
  Added missing heavy atom: .R<TSB 645>.A<C13 3>
  Added missing heavy atom: .R<TSB 645>.A<N6 10>
  Added missing heavy atom: .R<TSB 645>.A<O9 1>
  Added missing heavy atom: .R<TSB 645>.A<C14 5>
  Added missing heavy atom: .R<TSB 1288>.A<O3 16>
  Added missing heavy atom: .R<TSB 1288>.A<P1 17>
  Added missing heavy atom: .R<TSB 1288>.A<O6 18>
  Added missing heavy atom: .R<TSB 1288>.A<O7 19>
  Added missing heavy atom: .R<TSB 1288>.A<O2 20>
  Added missing heavy atom: .R<TSB 1288>.A<C10 21>
  Added missing heavy atom: .R<TSB 1288>.A<C7 24>
  Added missing heavy atom: .R<TSB 1288>.A<C8 25>
  Added missing heavy atom: .R<TSB 1288>.A<O1 34>
  Added missing heavy atom: .R<TSB 1288>.A<C9 26>
  Added missing heavy atom: .R<TSB 1288>.A<O4 30>
  Added missing heavy atom: .R<TSB 1288>.A<C6 35>
  Added missing heavy atom: .R<TSB 1288>.A<O5 27>
  Added missing heavy atom: .R<TSB 1288>.A<N1 37>
  Added missing heavy atom: .R<TSB 1288>.A<C2 38>
  Added missing heavy atom: .R<TSB 1288>.A<C1 41>
  Added missing heavy atom: .R<TSB 1288>.A<N2 39>
  Added missing heavy atom: .R<TSB 1288>.A<C3 42>
  Added missing heavy atom: .R<TSB 1288>.A<N3 50>
  Added missing heavy atom: .R<TSB 1288>.A<C5 43>
  Added missing heavy atom: .R<TSB 1288>.A<C4 48>
  Added missing heavy atom: .R<TSB 1288>.A<N5 44>
  Added missing heavy atom: .R<TSB 1288>.A<N4 47>
  Added missing heavy atom: .R<TSB 1289>.A<C11 14>
  Added missing heavy atom: .R<TSB 1289>.A<C12 9>
  Added missing heavy atom: .R<TSB 1289>.A<O8 15>
  Added missing heavy atom: .R<TSB 1289>.A<C13 3>
  Added missing heavy atom: .R<TSB 1289>.A<N6 10>
  Added missing heavy atom: .R<TSB 1289>.A<O9 1>
  Added missing heavy atom: .R<TSB 1289>.A<C14 5>
  total atoms in file: 10446
  Leap added 10292 missing atoms according to residue templates:
       60 Heavy
       10232 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.

  Solute vdw bounding box: 93.884 95.766 163.502
  Total bounding box for atom centers: 113.884 115.766 183.502
  Solvent unit box: 18.774 18.774 18.774
  Total vdw box size: 116.643 118.869 186.394 angstroms.
  Volume: 2584390.942 A^3
  Total mass 1402179.684 amu, Density 0.901 g/cc
  Added 69523 residues.
Checking Unit.
WARNING: There is a bond of 12.588304 angstroms between:
------- .R<TSB 644>.A<N3 50> and .R<TSB 645>.A<O9 1>
WARNING: There is a bond of 12.588500 angstroms between:
------- .R<TSB 1288>.A<N3 50> and .R<TSB 1289>.A<O9 1>
WARNING: The unperturbed charge of the unit: -33.999920 is not zero.

 -- ignoring the warnings.

Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: nb - oh
Could not find bond parameter for: nb - oh
Building angle parameters.
Could not find angle parameter: nb - oh - ho
Could not find angle parameter: nb - oh - c3
Could not find angle parameter: ca - nb - oh
Could not find angle parameter: ca - nb - oh
Could not find angle parameter: nb - oh - ho
Could not find angle parameter: nb - oh - c3
Could not find angle parameter: ca - nb - oh
Could not find angle parameter: ca - nb - oh
Building proper torsion parameters.
 ** No torsion terms for ca-nb-oh-ho
 ** No torsion terms for ca-nb-oh-c3
 ** No torsion terms for ca-nb-oh-ho
 ** No torsion terms for ca-nb-oh-c3
 ** No torsion terms for ca-nb-oh-ho
 ** No torsion terms for ca-nb-oh-c3
 ** No torsion terms for ca-nb-oh-ho
 ** No torsion terms for ca-nb-oh-c3
Building improper torsion parameters.
old PREP-specified impropers:
 <TSB 644>: C12 O8 C11 O3
 <TSB 644>: C6 C1 N1 C2
 <TSB 644>: H4 N1 C2 N2
 <TSB 644>: C3 N1 C1 N3
 <TSB 644>: C1 C5 C3 N2
 <TSB 644>: C3 N4 C5 N5
 <TSB 644>: C5 H1 N5 H2
 <TSB 644>: H3 N4 C4 N3
 <TSB 645>: C12 O8 C11 O3
 <TSB 645>: C6 C1 N1 C2
 <TSB 645>: H4 N1 C2 N2
 <TSB 645>: C3 N1 C1 N3
 <TSB 645>: C1 C5 C3 N2
 <TSB 645>: C3 N4 C5 N5
 <TSB 645>: C5 H1 N5 H2
 <TSB 645>: H3 N4 C4 N3
 <TSB 1288>: C12 O8 C11 O3
 <TSB 1288>: C6 C1 N1 C2
 <TSB 1288>: H4 N1 C2 N2
 <TSB 1288>: C3 N1 C1 N3
 <TSB 1288>: C1 C5 C3 N2
 <TSB 1288>: C3 N4 C5 N5
 <TSB 1288>: C5 H1 N5 H2
 <TSB 1288>: H3 N4 C4 N3
 <TSB 1289>: C12 O8 C11 O3
 <TSB 1289>: C6 C1 N1 C2
 <TSB 1289>: H4 N1 C2 N2
 <TSB 1289>: C3 N1 C1 N3
 <TSB 1289>: C1 C5 C3 N2
 <TSB 1289>: C3 N4 C5 N5
 <TSB 1289>: C5 H1 N5 H2
 <TSB 1289>: H3 N4 C4 N3
 total 4228 improper torsions applied
 32 improper torsions in old prep form
Building H-Bond parameters.
Parameter file was not saved.
        Quit
I would be grateful if you please help me understand where is the problem.
Thanks a lot in advance.

Sincere Regards,
Moitrayee Bhattacharyya
Prof. Saraswathi Vishveshwara Lab
Molecular Biophysics Unit
Indian Institute of Science
Bangalore
India.

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