AMBER Archive (2003)

Subject: Problem with a library

From: Frederico.Miranda_at_ibmb.uib.no
Date: Fri Jun 13 2003 - 15:27:36 CDT

Hye, I made a library for a phosphoserine based on the library for the serine
residue and the phosphate groups of nucleic acids residues (charges were
calculated for a phosphoserine). Here is my input file:

________________________________________________________________________________

    0 0 2

PHOSPHOSERINE
sep.db4
 SEP INT 1
 CORR OMIT DU BEG
   0.00000
   1 DUMM DU M 0 -1 -2 0.000 0.000 0.000 0.00000
   2 DUMM DU M 1 0 -1 1.449 0.000 0.000 0.00000
   3 DUMM DU M 2 1 0 1.522 111.100 0.000 0.00000
   4 N N M 3 2 1 1.335 116.600 180.000 -0.41570
   5 H H E 4 3 2 1.010 119.800 0.000 0.27190
   6 CA CT M 4 3 2 1.449 121.900 180.000 0.028
   7 HA H1 E 6 4 3 1.090 109.500 300.000 0.08430
   8 CB CT 3 6 4 3 1.525 111.100 60.000 0.105
   9 HB2 H1 E 8 6 4 1.090 109.500 300.000 0.066
  10 HB3 H1 E 8 6 4 1.090 109.500 60.000 0.066
  11 OG OS M 8 6 4 1.430 109.470 180.000 -0.491
  12 P P M 11 8 6 1.600 119.040 200.000 1.493
  13 O1P O2 E 12 11 8 1.480 109.610 180.000 -0.913
  14 O2P O2 E 12 11 8 1.480 109.580 60.000 -0.913
  15 O3P O2 E 12 11 8 1.480 109.590 300.000 -0.913
  16 C C M 6 4 3 1.522 111.100 180.000 0.59730
  17 O O E 16 6 4 1.229 120.500 0.000 -0.56790

IMPROPER
 -M CA N H
 CA +M C O
                                                                
DONE
STOP
________________________________________________________________________________

and here is the message that i get from leap:

__________

----- Source: ./leap.PO4_rPAH_dock.vacuum.030613.in
----- Source of ./leap.PO4_rPAH_dock.vacuum.030613.in done
----- Source: /disk2/software/amber7/dat/leap/cmd/leaprc.gaff
----- Source of /disk2/software/amber7/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /disk2/software/amber7/dat/leap/parm/gaff.dat
----- Source: /disk2/software/amber7/dat/leap/cmd/leaprc.ff94
----- Source of /disk2/software/amber7/dat/leap/cmd/leaprc.ff94 done
Log file: ./leap.log
Loading parameters: /disk2/software/amber7/dat/leap/parm/parm94.dat
Loading library: /disk2/software/amber7/dat/leap/lib/all_nucleic94.lib
Loading library: /disk2/software/amber7/dat/leap/lib/all_amino94.lib
Loading library: /disk2/software/amber7/dat/leap/lib/all_aminoct94.lib
Loading library: /disk2/software/amber7/dat/leap/lib/all_aminont94.lib
Loading library: /disk2/software/amber7/dat/leap/lib/ions94.lib
Loading library: /disk2/software/amber7/dat/leap/lib/solvents.lib
Loading Prep file: ./fred.SEP.in
Loading PDB file:
./PDB.rPAH_N-Terminal_PO4_Docked_From_Aurora_For_Amber.proton.pdb
  Added missing heavy atom: .R<ASP 137>.A<N 1>
  Added missing heavy atom: .R<CTHR 421>.A<OXT 15>
  total atoms in file: 6767
  Leap added 3 missing atoms according to residue templates:
       2 Heavy
       1 H / lone pairs
Checking Unit.
WARNING: There is a bond of 4.799280 angstroms between:
------- .R<SEP 16>.A<P 9> and .R<SEP 16>.A<C 13>
WARNING: There is a bond of 9.923259 angstroms between:
------- .R<LEU 136>.A<C 18> and .R<ASP 137>.A<N 1>
ERROR: The unperturbed charge of the unit: -10.502100 is not integral.
WARNING: The unperturbed charge of the unit: -10.502100 is not zero.

 -- ignoring the error and warnings.

Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: P - C
Building angle parameters.
Could not find angle parameter: O2 - P - C
Could not find angle parameter: O2 - P - C
Could not find angle parameter: O2 - P - C
Could not find angle parameter: P - C - O
Could not find angle parameter: P - C - N
Could not find angle parameter: OS - P - C
Building proper torsion parameters.
 ** No torsion terms for O2-P-C-O
 ** No torsion terms for O2-P-C-N
 ** No torsion terms for O2-P-C-O
 ** No torsion terms for O2-P-C-N
 ** No torsion terms for O2-P-C-O
 ** No torsion terms for O2-P-C-N
 ** No torsion terms for OS-P-C-O
 ** No torsion terms for OS-P-C-N
Building improper torsion parameters.
old PREP-specified impropers:
 <SEP 16>: -M CA N H
 <SEP 16>: CA +M C O
 total 1419 improper torsions applied
 2 improper torsions in old prep form
Building H-Bond parameters.
Parameter file was not saved.

______________

I don't understand what the problem is with the missing parameters, all of them
seem to be about a P - C connection, but there is no such binding in the file I
have created. If someone could help me, please... Thank you.

                                           Frederico Miranda