AMBER Archive (2007)

Subject: AMBER: leaprc.ff02polEP.r1into xleap

From: Denis Courtier (amber982_at_gmail.com)
Date: Wed Nov 28 2007 - 11:44:21 CST

Hello,

As dac recommended to me.I have used leaprc.ff02polEP.r1. I used the
following command.

$AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff02pol.r1

Obtaining:

Welcome to LEaP!
Sourcing: /usr/local/amber9/dat/leap/cmd/leaprc.ff02pol.r1
Log file: ./leap.log
Loading parameters: /usr/local/amber9/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02
/04/99
Loading parameters: /usr/local/amber9/dat/leap/parm/frcmod.ff02pol.r1
Reading force field modification type file (frcmod)
Reading title:
DISABLE BACKBONE AND NO-HYDROGEN
Loading library: /usr/local/amber9/dat/leap/lib/all_nucleic02.lib
Loading library: /usr/local/amber9/dat/leap/lib/all_amino02.r1.lib
Loading library: /usr/local/amber9/dat/leap/lib/all_aminoct02.lib
Loading library: /usr/local/amber9/dat/leap/lib/all_aminont02.lib
Loading library: /usr/local/amber9/dat/leap/lib/ions94.lib
Loading library: /usr/local/amber9/dat/leap/lib/solvents.lib

Now, i loaded my pdb file.

> napro=loadpdb napro.pdb

Loading PDB file: ./napro.pdb
Warning: name change in pdb file residue 1 ;
 this residue is split into ACE and PRO.
1 residues had naming warnings.
 There are split residues;
 residue sequence numbers will not correspond to those in the pdb.
Created a new atom named: C10 within residue: .R<ACE 1>
Created a new atom named: C11 within residue: .R<ACE 1>
Created a new atom named: O12 within residue: .R<ACE 1>
Created a new atom named: H20 within residue: .R<ACE 1>
Created a new atom named: H21 within residue: .R<ACE 1>
Created a new atom named: H22 within residue: .R<ACE 1>
  Added missing heavy atom: .R<ACE 1>.A<O 6>
  Added missing heavy atom: .R<ACE 1>.A<C 5>
  Added missing heavy atom: .R<ACE 1>.A<CH3 2>
Created a new atom named: C1 within residue: .R<CPRO 2>
Created a new atom named: N2 within residue: .R<CPRO 2>
Created a new atom named: C3 within residue: .R<CPRO 2>
Created a new atom named: C4 within residue: .R<CPRO 2>
Created a new atom named: O5 within residue: .R<CPRO 2>
Created a new atom named: C6 within residue: .R<CPRO 2>
Created a new atom named: C7 within residue: .R<CPRO 2>
Created a new atom named: O8 within residue: .R<CPRO 2>
Created a new atom named: H9 within residue: .R<CPRO 2>
Created a new atom named: H13 within residue: .R<CPRO 2>
Created a new atom named: H14 within residue: .R<CPRO 2>
Created a new atom named: H15 within residue: .R<CPRO 2>
Created a new atom named: H16 within residue: .R<CPRO 2>
Created a new atom named: H17 within residue: .R<CPRO 2>
Created a new atom named: H18 within residue: .R<CPRO 2>
Created a new atom named: H19 within residue: .R<CPRO 2>
  Added missing heavy atom: .R<CPRO 2>.A<N 1>
  Added missing heavy atom: .R<CPRO 2>.A<CD 2>
  Added missing heavy atom: .R<CPRO 2>.A<CA 11>
  Added missing heavy atom: .R<CPRO 2>.A<CG 5>
  Added missing heavy atom: .R<CPRO 2>.A<CB 8>
  Added missing heavy atom: .R<CPRO 2>.A<C 13>
  Added missing heavy atom: .R<CPRO 2>.A<O 14>
  Added missing heavy atom: .R<CPRO 2>.A<OXT 15>
  total atoms in file: 22
  Leap added 21 missing atoms according to residue templates:
       11 Heavy
       10 H / lone pairs
  The file contained 22 atoms not in residue templates

Then, I created a water-box.

> solvatebox napro POL3BOX 11
 (using default radius 1.500000 for C10)
 (using default radius 1.500000 for C11)
 (using default radius 1.500000 for O12)
 (using default radius 1.500000 for C1)
 (using default radius 1.500000 for N2)
 (using default radius 1.500000 for C3)
 (using default radius 1.500000 for C4)
 (using default radius 1.500000 for O5)
 (using default radius 1.500000 for C6)
 (using default radius 1.500000 for C7)
 (using default radius 1.500000 for O8)
  Solute vdw bounding box: 10.275 9.118 8.816
  Total bounding box for atom centers: 32.275 31.118 30.816
  Solvent unit box: 18.642 18.642 18.642
 (using default radius 1.500000 for C10)
 (using default radius 1.500000 for C11)
 (using default radius 1.500000 for O12)
 (using default radius 1.500000 for C1)
 (using default radius 1.500000 for N2)
 (using default radius 1.500000 for C3)
 (using default radius 1.500000 for C4)
(using default radius 1.500000 for O5)
 (using default radius 1.500000 for C6)
 (using default radius 1.500000 for C7)
 (using default radius 1.500000 for O8)
  Total vdw box size: 35.357 34.098 34.069 angstroms.
  Volume: 41072.259 A^3
  Mass > 16965.088 amu, Density > 0.686 g/cc
      (type - hence mass - of one or more atoms could not be found)
  Added 933 residues.

Finally, I tried to created my prmtop and inpcrd files.

> saveamberparmpol napro napro.prmtop napro.inpcrd
Checking Unit.
WARNING: The unperturbed charge of the unit: -1.000000 is not zero.
FATAL: Atom .R<ACE 1>.A<C10 7> does not have a type.
FATAL: Atom .R<ACE 1>.A<C11 8> does not have a type.
FATAL: Atom .R<ACE 1>.A<O12 9> does not have a type.
FATAL: Atom .R<ACE 1>.A<H20 10> does not have a type.
FATAL: Atom .R<ACE 1>.A<H21 11> does not have a type.
FATAL: Atom .R<ACE 1>.A<H22 12> does not have a type.
FATAL: Atom .R<CPRO 2>.A<C1 16> does not have a type.
FATAL: Atom .R<CPRO 2>.A<N2 17> does not have a type.
FATAL: Atom .R<CPRO 2>.A<C3 18> does not have a type.
FATAL: Atom .R<CPRO 2>.A<C4 19> does not have a type.
FATAL: Atom .R<CPRO 2>.A<O5 20> does not have a type.
FATAL: Atom .R<CPRO 2>.A<C6 21> does not have a type.
FATAL: Atom .R<CPRO 2>.A<C7 22> does not have a type.
FATAL: Atom .R<CPRO 2>.A<O8 23> does not have a type.
FATAL: Atom .R<CPRO 2>.A<H9 24> does not have a type.
FATAL: Atom .R<CPRO 2>.A<H13 25> does not have a type.
FATAL: Atom .R<CPRO 2>.A<H14 26> does not have a type.
FATAL: Atom .R<CPRO 2>.A<H15 27> does not have a type.
FATAL: Atom .R<CPRO 2>.A<H16 28> does not have a type.
FATAL: Atom .R<CPRO 2>.A<H17 29> does not have a type.
FATAL: Atom .R<CPRO 2>.A<H18 30> does not have a type.
FATAL: Atom .R<CPRO 2>.A<H19 31> does not have a type.
Failed to generate parameters
Parameter file was not saved.

But i could not get it. Can anybody explain me what i am doing wrong?

My pdb file is:

HEADER CSD ENTRY naprot_amber02.mol
CRYST1 1.0000 1.0000 1.0000 90.00 90.00 90.00 Unknown
SCALE1 1.000000 -0.000000 -0.000000 0.000000
SCALE2 0.000000 1.000000 -0.000000 0.000000
SCALE3 0.000000 0.000000 1.000000 0.000000
HETATM 10 C10 ACE 1 -1.465 -1.291 2.420 1.00 0.00
C
HETATM 11 C11 ACE 1 -1.582 -0.658 1.045 1.00 0.00
C
HETATM 12 O12 ACE 1 -2.634 -0.645 0.449 1.00 0.00
O
HETATM 20 H20 ACE 1 -0.833 -2.207 2.373 1.00 0.00
H
HETATM 21 H21 ACE 1 -1.035 -0.576 3.158 1.00 0.00
H
HETATM 22 H22 ACE 1 -2.470 -1.592 2.794 1.00 0.00
H
HETATM 1 C1 PRO 1 0.836 -0.047 1.140 1.00 0.00
C
HETATM 2 N2 PRO 1 -0.475 -0.098 0.496 1.00 0.00
N
HETATM 3 C3 PRO 1 -0.504 0.557 -0.814 1.00 0.00
C
HETATM 4 C4 PRO 1 -0.537 -0.399 -1.992 1.00 0.00
C
HETATM 5 O5 PRO 1 -0.546 -0.087 -3.158 1.00 0.00
O
HETATM 6 C6 PRO 1 0.794 1.386 -0.787 1.00 0.00
C
HETATM 7 C7 PRO 1 1.746 0.497 0.027 1.00 0.00
C
HETATM 8 O8 PRO 1 -0.507 -1.678 -1.607 1.00 0.00
O
HETATM 9 H9 PRO 1 -0.528 -2.341 -2.316 1.00 0.00
H
HETATM 13 H13 PRO 1 1.172 -1.052 1.485 1.00 0.00
H
HETATM 14 H14 PRO 1 0.797 0.666 1.997 1.00 0.00
H
HETATM 15 H15 PRO 1 -1.388 1.233 -0.903 1.00 0.00
H
HETATM 16 H16 PRO 1 1.185 1.636 -1.802 1.00 0.00
H
HETATM 17 H17 PRO 1 0.625 2.341 -0.234 1.00 0.00
H
HETATM 18 H18 PRO 1 2.107 -0.341 -0.617 1.00 0.00
H
HETATM 19 H19 PRO 1 2.634 1.047 0.420 1.00 0.00
H
CONECT 1 2 7 13 14
CONECT 2 1 3 11
CONECT 3 2 4 6 15
CONECT 4 3 5 8
CONECT 5 4
CONECT 6 3 7 16 17
CONECT 7 1 6 18 19
CONECT 8 4 9
CONECT 9 8
CONECT 10 11 20 21 22
CONECT 11 2 10 12
CONECT 12 11
CONECT 13 1
CONECT 14 1
CONECT 15 3
CONECT 16 6
CONECT 17 6
CONECT 18 7
CONECT 19 7
CONECT 20 10
CONECT 21 10
CONECT 22 10
MASTER 0 0 0 0 0 0 0 0 3 22 0 22 0
END

Thank you.

Denis.

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