AMBER Archive (2004)

Subject: AMBER: Build a H+ ion in Leap?

From: Xin Chen (
Date: Thu Feb 19 2004 - 13:40:40 CST

Similar to the codes used in amber7/dat/leap/lib/ions94.cmd to build Li+, I
build a H+ to change the pH value of a solution:

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

After I use addions to add it and then saveAmberParm, there is segmentation
fault, while if I add a Li+ instead, there is nothing wrong. Something must
be wrong when I create the H+, what is it? Thanks! I have patch the bugfix
2,8,18,21 for my AMBER 7.

> 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.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

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