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.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
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Received on Thu Feb 19 2004 - 19:53:01 PST
