AMBER Archive (2004)

Subject: AMBER: Segmentation fault in SaveAmberParm

From: xinchen (xinchen_at_ic.sunysb.edu)
Date: Tue Feb 17 2004 - 21:31:35 CST

Hi,

When I tried to add H+ to a solution and then saveamberparm, I met
segmentation fault, while when I tried Li+, there is no problem. It
seems
not to be a memory problem, and I have patch the bugfix 2,8,18,21 for my
AMBER 7.
After I add H+, I can save to pdb, but cannot saveamberparm:

> x1 = loadpdb 1UBQ.pdb
Loading PDB file: 1UBQ.pdb
  total atoms in file: 660
  Leap added 745 missing atoms according to residue templates:
       745 H / lone pairs
> addions x1 H+ 1
Adding 1 counter ions to "x1" using 1A grid
Grid extends from solute vdw + 0.60 to 6.60
Resolution: 1.00 Angstrom.
grid build: 0 sec
Solvent present: replacing closest with ion
         when steric overlaps occur
Calculating grid charges
charges: 3 sec
(No solvent overlap)
Placed H+ in x1 at (37.84, 16.29, 19.03).

Done adding ions.
> savepdb x1 x2.pdb
Writing pdb file: x2.pdb
 Shortening residue name for PDB format: NMET -> MET
 Shortening residue name for PDB format: CGLY -> GLY
> saveamberparm x1 x1.top x1.crd
Checking Unit.
WARNING: The unperturbed charge of the unit: 1.000000 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 216 improper torsions applied
Building H-Bond parameters.
Marking per-residue atom chain types.
  (Residues lacking connect0/connect1 -
   these don't have chain types marked:

        res total affected

        CGLY 1
        NMET 1
        WAT 58
  )
 (no restraints)
Segmentation fault

/////The H+ ion was created using codes:

i = createAtom H+ H 1.0
set i element H
set i position { 0 0 0 }
r = createResidue H+
add r i
H+ = createUnit H+
add H+ r
saveOff H+ ./ions94.lib

/////When I add Li+, there is no problem:

> x1 = loadpdb /home/xin/1UBQ.pdb
Loading PDB file: /home/xin/1UBQ.pdb
  total atoms in file: 660
  Leap added 745 missing atoms according to residue templates:
       745 H / lone pairs
> addions x1 Li+ 1
Adding 1 counter ions to "x1" using 1A grid
Grid extends from solute vdw + 1.14 to 7.14
Resolution: 1.00 Angstrom.
grid build: 1 sec
Solvent present: replacing closest with ion
         when steric overlaps occur
Calculating grid charges
charges: 2 sec
(No solvent overlap)
Placed Li+ in x1 at (45.30, 29.75, 7.50).

Done adding ions.
> savepdb x1 x2.pdb
Writing pdb file: x2.pdb
 Shortening residue name for PDB format: NMET -> MET
 Shortening residue name for PDB format: CGLY -> GLY
> saveamberparm x1 x1.top x1.crd
Checking Unit.
WARNING: The unperturbed charge of the unit: 1.000000 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 216 improper torsions applied
Building H-Bond parameters.
Marking per-residue atom chain types.
  (Residues lacking connect0/connect1 -
   these don't have chain types marked:

        res total affected

        CGLY 1
        NMET 1
        WAT 58
  )
 (no restraints)
>

//////Any suggestions? Thank you so much in advance!

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