AMBER Archive (2009)

Subject: [AMBER] NATOM in prmtop and inpcrd files does not agree with the input

From: Maria Mirza (maryamirza_at_gmail.com)
Date: Mon Aug 24 2009 - 23:41:39 CDT

Hello,

I am trying to debug some errors during sander runs. One thing that I am
noticing is that both my crd and prmtop files have NATOM which do not agree
with the input at all.
The actual pdb has 1994 atoms, leap adds 2 missing heavy atoms. yet both the
prmtop and crd files somehow have 4012 atoms listed.

> rec = loadpdb 1BVR_protonly.pdb
Loading PDB file: ./1BVR_protonly.pdb
  Added missing heavy atom: .R<NTHR 2>.A<CG2 9>
  Added missing heavy atom: .R<NTHR 2>.A<OG1 13>
  total atoms in file: 1994
  Leap added 2018 missing atoms according to residue templates:
       2 Heavy
       2016 H / lone pairs
> saveamberparm rec rec.prmtop rec.inpcrd
Checking Unit.
WARNING: The unperturbed charge of the unit: -4.000000 is not zero.

 -- ignoring the warning.

Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 775 improper torsions applied
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
  (Residues lacking connect0/connect1 -
   these don't have chain types marked:

        res total affected

        CLEU 1
        NTHR 1
  )
 (no restraints)
>

Yet on the prmtop file I see
%VERSION VERSION_STAMP = V0001.000 DATE = 08/25/09 00:37:57
%FLAG TITLE
%FORMAT(20a4)

%FLAG POINTERS
%FORMAT(10I8)
    4012 14 2016 2034 4580 2763 8607 7024
0 0
   22113 268 2034 2763 7024 41 89 42
28 0
       0 0 0 0 0 0 0 0
24 0
       0

Similarly,

  4012
   6.5910000 1.0040000 39.3800000 6.4678657 1.9422191 39.0268940
   7.5753742 0.7783801 39.3657368 6.0630818 0.9072826 40.2355978
   5.9520000 0.0530000 38.4100000 6.6822220 -0.6468279 38.0036554
   4.8390000 -0.7470000 39.1050000 4.3643746 -1.4122597 38.3837091
   5.4382009 -1.5718274 40.2391263 5.9126350 -0.9071757 40.9611028

in the crd file. Is this an error, and if so, any ideas why this is
occuring? (I have tried this with multiple pdb files for the same target, to
no avail.)

Thanks
Maria 

-- 
Only 'No Differences' can make a difference.
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