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
On 05/26/2012 07:16 AM, M wrote: > 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)?
The CHARMM force field in Modeller is fundamentally the same as in CHARMM 22 itself, so this is unlikely to be the problem. The other terms in the force field derive from the alignment, so if your model is poor either the problem really is in the alignment or the optimizer failed to satisfy all the restraints. The latter problem is generally solved by building a larger number of models.
Ben Webb, Modeller Caretaker
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Modeller Caretaker