AMBER Archive (2004)

Subject: AMBER: segmentation fault in Leap

From: Ioana Cozmuta (
Date: Tue Jan 20 2004 - 22:39:28 CST

Hi amber users,

I am trying to add 10 ions to neutralize a structure in Leap. My structure
has 3361 atoms in the protein residues, 27521 water residues, 384 K+ ions and 358
Cl- ions.

I do not have any error loading the structure, leap is adding the missing
hydrogens but then after the grid charge calculation, when it tries to
place the first ion I get a segmentation fault error.

Here are the last lines in my output file:

  total atoms in file: 27521
  Leap added 50006 missing atoms according to residue templates:
       50006 H / lone pairs
> charge foo
Total unperturbed charge: 10.00 Total perturbed charge: 10.00
> addIons foo Cl- 0
10 Cl- ions required to neutralize.
Adding 10 counter ions to "foo" using 1A grid
Total solute charge: 10.00
Max atom radius: 2.27 Grid extends from solute vdw + 2.27 to 8.54
Box: enclosing: -23.23 -22.87 -11.39 87.23 87.37 100.41
   sized: 104.77 105.13 116.61
   edge: 128.00
Resolution: 1.00 Angstrom.
Tree depth: 7 grid build: 11 sec
Volume = 27.18% of box, grid points 569954
Solvent present: replacing closest with ion when steric overlaps occur
Calculating grid charges charges: 4004 sec (Replacing solvent molecule)
Placed Cl- in foo at (34.61, -13.78, 49.32).
Segmentation fault (core dumped)

Does anyone have any idea what may be wrong in this case? Could it be that
there is a memory problem?

Thank you,

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