[modeller_usage] short interatomic distances

[M <>]

Hello,

I have a problem concerning the step of evaluating my model. I'm using the whatif server (http://swift.cmbi.ru.nl/servers/html/index.html). Most of the scores are fine, but there are many abnormally short interatomic distances according to whatif. The problem doesn't result from the alignment. Is it possible that it is a result of different parametrization used by modeller (or by the implemented CHARMM force field)? 

Below is an enclosed example of the whatif log file concerning the short distances (two columns from the end with numbers are important: the first number in the table tells how much shorter that specific contact is than the acceptable limit, the second distance is the distance between the centres of the two atoms):

  15 ILE   (  15-)  A      CG2 <->   59 MET   (  59-)  A      SD     0.33    3.07  INTRA BF
 179 MET   ( 179-)  A      SD  <->  207 VAL   ( 207-)  B      CG1    0.31    3.09  INTRA BL
  19 THR   (  19-)  A      N   <->  252 LEU   ( 252-)  B      CD2    0.28    2.82  INTRA BF
  19 THR   (  19-)  A      CG2 <->   55 ALA   (  55-)  A      CB     0.27    2.93  INTRA BF
 154 VAL   ( 154-)  A      CG2 <->  156 LEU   ( 156-)  A      CD2    0.27    2.93  INTRA BF
 217 PHE   ( 217-)  B      CE1 <->  244 LEU   ( 244-)  B      CD2    0.27    2.93  INTRA BF
 105 TYR   ( 105-)  A      CA  <->  186 ILE   ( 186-)  A      CD1    0.27    2.93  INTRA BF
 138 THR   ( 138-)  A      CG2 <->  139 LEU   ( 139-)  A      CD1    0.26    2.94  INTRA BF
 258 TYR   ( 258-)  B      CB  <->  265 LEU   ( 265-)  B      CD1    0.26    2.94  INTRA BF
  19 THR   (  19-)  A      CB  <->  252 LEU   ( 252-)  B      CD2    0.26    2.94  INTRA BF
  65 THR   (  65-)  A      CG2 <->   72 TRP   (  72-)  A      CE3    0.26    2.94  INTRA BF
 179 MET   ( 179-)  A      CE  <->  207 VAL   ( 207-)  B      CG1    0.25    2.95  INTRA BL
 239 VAL   ( 239-)  B      CG1 <->  243 PHE   ( 243-)  B      CE2    0.25    2.95  INTRA BF
 256 PHE   ( 256-)  B      CE2 <->  260 PHE   ( 260-)  B      CZ     0.25    2.95  INTRA BF
 220 LEU   ( 220-)  B      CD1 <->  235 ILE   ( 235-)  B      CG1    0.25    2.95  INTRA BF
  73 ILE   (  73-)  A      CD1 <->   74 PHE   (  74-)  A      CD1    0.25    2.95  INTRA BF
  33 VAL   (  33-)  A      CG1 <->   35 LYS   (  35-)  A      CG     0.25    2.95  INTRA BL
  25 LEU   (  25-)  A      CD2 <->  269 TYR   ( 269-)  B      CD1    0.25    2.95  INTRA BL
  65 THR   (  65-)  A      CG2 <->   72 TRP   (  72-)  A      CZ3    0.25    2.95  INTRA BF

this is not a full list (fortunately other values are better, deviation from the acceptable value is small).

Best regards,

Mat