I used top to find that there is no big memory usage during the process. So
I think it's not a momery problem. I think there is something wrong when I
create the H+ since there is nothing wrong if I use Li+ instead. Could
someone help me to check the code I used to create the H+ ion? Thank you so
much.
----- Original Message -----
From: "xinchen" <xinchen.ic.sunysb.edu>
To: <amber.scripps.edu>
Sent: Tuesday, February 17, 2004 10:31 PM
Subject: AMBER: Segmentation fault in SaveAmberParm
> 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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Received on Wed Feb 18 2004 - 19:53:01 PST
