AMBER Archive (2009)

Subject: [AMBER] tleap errors !!

From: Sampath Koppole (sampathkoppole_at_yahoo.com)
Date: Thu Feb 26 2009 - 03:47:48 CST

Dear All,
I am trying to import a pdb file into amber using tleap.

Everything seems normal on the screen-log (pasted below !!) but in the leap.log file that was created,
I have a few errors like the following when I save the prmtop and the initial coordinates:
-----------------------------------------------------------------------------------------------------------
> saveamberparm bvc bvc/bvc.prmtop bvc/bvc.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA
        atoms are: CG CE2 CD2 CE3
 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB
        atoms are: NE1 CZ2 CE2 CD2
 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA
        atoms are: CG CE2 CD2 CE3
 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB
        atoms are: NE1 CZ2 CE2 CD2
 ** Warning: No sp2 improper torsion term for C*-CN-CB-CA
        atoms are: CG CE2 CD2 CE3
 ** Warning: No sp2 improper torsion term for NA-CA-CN-CB
        atoms are: NE1 CZ2 CE2 CD2
 total 488 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

        WAT 6791
  )
 (no restraints)
-----------------------------------------------------------------------------------------------------------
Should I be bothered ?

Thanks for your time ...
Cheers,
Sampath.

PS: For you reference, here are the messages that came on the screen while I was importing bvc into amber.
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------
> bvc = loadpdb bvc/bvc-final.pdb
Loading PDB file: ./bvc/bvc-final.pdb
  total atoms in file: 1238
  Leap added 1284 missing atoms according to residue templates:
       1284 H / lone pairs
> solvatebox bvc TIP3PBOX 10
  Solute vdw bounding box: 45.403 42.502 41.805
  Total bounding box for atom centers: 65.403 62.502 61.805
  Solvent unit box: 18.774 18.774 18.774
  Total vdw box size: 68.705 65.919 65.030 angstroms.
  Volume: 294513.583 A^3
  Total mass 139472.456 amu, Density 0.786 g/cc
  Added 6759 residues.
> check bvc
Checking 'bvc'....
WARNING: The unperturbed charge of the unit: 5.000000 is not zero.
Warning: Close contact of 1.856908 angstroms between .R<GLU 22>.A<OE2 13> and .R<ARG 48>.A<HE 15>
Warning: Close contact of 2.158592 angstroms between .R<GLN 23>.A<HE22 15> and .R<WAT 175>.A<H1 2>
Warning: Close contact of 1.830095 angstroms between .R<SER 40>.A<HG 9> and .R<WAT 158>.A<H2 3>
Warning: Close contact of 1.628582 angstroms between .R<ARG 67>.A<HH11 18> and .R<WAT 180>.A<H2 3>
Warning: Close contact of 1.055309 angstroms between .R<GLU 122>.A<H 2> and .R<WAT 183>.A<H2 3>
Warning: Close contact of 1.725712 angstroms between .R<WAT 162>.A<H2 3> and .R<WAT 174>.A<H1 2>
Checking parameters for unit 'bvc'.
Checking for bond parameters.
Checking for angle parameters.
check: Warnings: 7
Unit is OK.
> addions2 bvc Cl- 0
5 Cl- ions required to neutralize.
Adding 5 counter ions to "bvc" using 1A grid
Grid extends from solute vdw + 2.47 to 8.47
Resolution: 1.00 Angstrom.
grid build: 2 sec
Calculating grid charges
charges: 326 sec
Placed Cl- in bvc at (27.81, -18.66, -33.38).
Placed Cl- in bvc at (28.81, -33.66, 15.62).
Placed Cl- in bvc at (-8.19, -33.66, -3.38).
Placed Cl- in bvc at (4.81, 26.34, 32.62).
Placed Cl- in bvc at (-34.19, -13.66, -12.38).

Done adding ions.
> saveamberparm bvc bvc/bvc.prmtop bvc/bvc.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 488 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

        WAT 6791
  )
 (no restraints)
-------------------------------------------------------------------------------------------------------------------------------------------------------------------------

      

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