ADL: Missing P-O bond

Mihaly Mezei Mihaly.Mezei at mssm.edu
Mon May 22 15:35:50 PDT 2006


Greetings,

it looks like a bug to me. I just had a look at the autgrid3 code calculating the bonds to an oxygen and it is only prepared to deal with oxygens bound to a carbon or a hydrogen. Around line 964 in my copy of main.c in the autogrid3 source directory it says

  if (((rd2 < 2.89) && (atomtype[ib] == CARBON)) ||
      ((rd2 < 1.69) && (atomtype[ib] == HYDROGEN))) {
                    if (nbond == 2) {
 
There is no provision for anyhing else. I would change it to 
 if (((rd2 < 2.89) && (atomtype[ib] == CARBON)) ||
      ((rd2 < x.xx && (atomtype[ib] == XXXXXX)) ||    
      ((rd2 < 1.69) && (atomtype[ib] == HYDROGEN))) {
                    if (nbond == 2) {
 
where XXXXXX is the name of the atom type assigned to P (in autogrid.h) and x.xx is the distance threshold for the P-O bond.

(Garret, am I right?)

Mihaly Mezei

Department of Molecular Physiology & Biophysics, Mount Sinai School of Medicine, NYU
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