Dear all: When I get the models from modeller, there are always some atom clash。How to solve this problem? Could modeller solve this by itself? I get models from "model-changeopt.py", and set a.md_level = refine.slow a.repeat_optimization = 50 Here is the results for the best model:
Strongest energies for the vdWaals interactions _____________________________ _______________
1 236 .GLU.N - 236 .GLU.CD 2.697 1.7143 2 318 .ASP.CG - 318 .ASP.C 2.844 1.7121 3 278 .ASP.CG - 278 .ASP.C 2.845 1.7029 4 99 .ASP.O - 101 .ASN.N 2.532 1.6450 5 143 .ARG.O - 161 .GLY.N 2.547 1.4700 6 250 .TYR.CG - 250 .TYR.C 2.885 1.3172 7 244 .ASP.O - 248 .ASP.N 2.563 1.3145 8 214 .ASP.CG - 214 .ASP.C 2.888 1.2951 9 411 .THR.O - 412 .LEU.C 2.710 1.2663 10 385 .ALA.O - 386 .ASP.C 2.713 1.2380 11 244 .ASP.N - 249 .ARG.O 2.578 1.1794 12 275 .SER.HA - 285 .ILE.O 2.185 1.1460 13 294 .ASP.O - 295 .GLY.C 2.725 1.1418 14 289 .TRP.CG - 289 .TRP.C 2.907 1.1394 15 276 .PHE.CG - 276 .PHE.C 2.914 1.0910
_____________________________________________________________________________
Strongest energies for the H-bonds interactions ____________________________________________
1 344 .ASN.HD21- 344 .ASN.O 1.850 -1.5000 2 442 .ALA.O - 445 .SER.H 1.850 -1.5000 3 96 .GLY.O - 105 .VAL.H 1.850 -1.5000 4 397 .GLY.O - 399 .THR.H 1.850 -1.5000 5 230 .LEU.H - 235 .PHE.O 1.850 -1.5000 6 134 .ASP.OD2 - 164 .ARG.HH12 1.850 -1.5000 7 353 .ILE.O - 511 .ALA.H 1.850 -1.5000 8 398 .SER.HG - 398 .SER.O 1.849 -1.5000 9 106 .GLN.HE22- 142 .PHE.O 1.849 -1.5000 10 71 .PRO.O - 74 .LYS.H 1.849 -1.5000 11 206 .SER.HG - 208 .GLN.O 1.848 -1.4999 12 478 .ASP.O - 480 .SER.H 1.848 -1.4999 13 365 .VAL.O - 475 .SER.H 1.852 -1.4999 14 56 .LEU.O - 59 .TRP.HE1 1.848 -1.4999 15 177 .ASN.OD1 - 180 .LYS.H 1.852 -1.4999
_____________________________________________________________________________
Strongest energies for the Elect. interactions ____________________________________________
1 31 .HIS.HE2 - 117 .PRO.O 1.872 -6.9175 2 50 .HIS.HE2 - 118 .TYR.O 1.940 -6.4947 3 406 .PRO.O - 513 .ASN.OD1 2.707 6.0365 4 348 .ASP.O - 513 .ASN.O 2.771 5.8644 5 294 .ASP.O - 295 .GLY.C 2.725 -5.8603 6 385 .ALA.O - 386 .ASP.C 2.713 -5.8427 7 340 .VAL.O - 524 .LEU.O 2.774 5.7495 8 411 .THR.O - 412 .LEU.C 2.710 -5.7430 9 326 .GLN.O - 488 .GLY.O 2.738 5.6908 10 9 .HIS.HE2 - 483 .GLU.OE2 1.871 -5.6896 11 134 .ASP.O - 135 .ILE.C 2.798 -5.6414 12 201 .ASP.O - 225 .VAL.O 2.878 5.5602 13 362 .GLN.OE1 - 530 .ASP.O 2.901 5.5484 14 386 .ASP.O - 387 .LEU.C 2.822 -5.5457 15 441 .ASP.CG - 441 .ASP.O 2.899 -5.4778
_____________________________________________________________________________
Non-bonded contributions _________________________
Normal pairs
H-bonds : N.pairs= 14516 energy= -861. Elect. : N.pairs= 687078 energy= -0.402E+04 vdWaals : N.pairs= 699117 energy= -0.443E+04
1-4 pairs H-bonds : N.pairs= 5 energy= -0.137 Elect. : N.pairs= 21311 energy= 0.430E+04 vdWaals : N.pairs= 21306 energy= 288.
Total H-bonds : N.pairs= 14521 energy= -861. Elect. : N.pairs= 708389 energy= 282. vdWaals : N.pairs= 720423 energy= -0.414E+04
Total non-bonded energy : -0.472E+04
Does anybody knows how to solve this problem? My template identiy>50%, similarity>80%, the problem is still there.... I don't know why. Enven if I set the MD to "slow_large".........
在2009-11-27,leuven leuven@yeah.net 写道:
-----原始邮件----- 发件人:leuven leuven@yeah.net 发送时间:2009年11月27日 星期五 收件人:modeller_usage modeller_usage@salilab.org 主题:[modeller_usage] atom clashed
Dear all: When I get the models from modeller, there are always some atom clash。How to solve this problem? Could modeller solve this by itself? I get models from "model-changeopt.py", and set a.md_level = refine.slow a.repeat_optimization = 50 Here is the results for the best model:
Strongest energies for the vdWaals interactions _____________________________ _______________
1 236 .GLU.N - 236 .GLU.CD 2.697 1.7143 2 318 .ASP.CG - 318 .ASP.C 2.844 1.7121 3 278 .ASP.CG - 278 .ASP.C 2.845 1.7029 4 99 .ASP.O - 101 .ASN.N 2.532 1.6450 5 143 .ARG.O - 161 .GLY.N 2.547 1.4700 6 250 .TYR.CG - 250 .TYR.C 2.885 1.3172 7 244 .ASP.O - 248 .ASP.N 2.563 1.3145 8 214 .ASP.CG - 214 .ASP.C 2.888 1.2951 9 411 .THR.O - 412 .LEU.C 2.710 1.2663 10 385 .ALA.O - 386 .ASP.C 2.713 1.2380 11 244 .ASP.N - 249 .ARG.O 2.578 1.1794 12 275 .SER.HA - 285 .ILE.O 2.185 1.1460 13 294 .ASP.O - 295 .GLY.C 2.725 1.1418 14 289 .TRP.CG - 289 .TRP.C 2.907 1.1394 15 276 .PHE.CG - 276 .PHE.C 2.914 1.0910
_____________________________________________________________________________
Strongest energies for the H-bonds interactions ____________________________________________
1 344 .ASN.HD21- 344 .ASN.O 1.850 -1.5000 2 442 .ALA.O - 445 .SER.H 1.850 -1.5000 3 96 .GLY.O - 105 .VAL.H 1.850 -1.5000 4 397 .GLY.O - 399 .THR.H 1.850 -1.5000 5 230 .LEU.H - 235 .PHE.O 1.850 -1.5000 6 134 .ASP.OD2 - 164 .ARG.HH12 1.850 -1.5000 7 353 .ILE.O - 511 .ALA.H 1.850 -1.5000 8 398 .SER.HG - 398 .SER.O 1.849 -1.5000 9 106 .GLN.HE22- 142 .PHE.O 1.849 -1.5000 10 71 .PRO.O - 74 .LYS.H 1.849 -1.5000 11 206 .SER.HG - 208 .GLN.O 1.848 -1.4999 12 478 .ASP.O - 480 .SER.H 1.848 -1.4999 13 365 .VAL.O - 475 .SER.H 1.852 -1.4999 14 56 .LEU.O - 59 .TRP.HE1 1.848 -1.4999 15 177 .ASN.OD1 - 180 .LYS.H 1.852 -1.4999
_____________________________________________________________________________
Strongest energies for the Elect. interactions ____________________________________________
1 31 .HIS.HE2 - 117 .PRO.O 1.872 -6.9175 2 50 .HIS.HE2 - 118 .TYR.O 1.940 -6.4947 3 406 .PRO.O - 513 .ASN.OD1 2.707 6.0365 4 348 .ASP.O - 513 .ASN.O 2.771 5.8644 5 294 .ASP.O - 295 .GLY.C 2.725 -5.8603 6 385 .ALA.O - 386 .ASP.C 2.713 -5.8427 7 340 .VAL.O - 524 .LEU.O 2.774 5.7495 8 411 .THR.O - 412 .LEU.C 2.710 -5.7430 9 326 .GLN.O - 488 .GLY.O 2.738 5.6908 10 9 .HIS.HE2 - 483 .GLU.OE2 1.871 -5.6896 11 134 .ASP.O - 135 .ILE.C 2.798 -5.6414 12 201 .ASP.O - 225 .VAL.O 2.878 5.5602 13 362 .GLN.OE1 - 530 .ASP.O 2.901 5.5484 14 386 .ASP.O - 387 .LEU.C 2.822 -5.5457 15 441 .ASP.CG - 441 .ASP.O 2.899 -5.4778
_____________________________________________________________________________
Non-bonded contributions _________________________
Normal pairs
H-bonds : N.pairs= 14516 energy= -861. Elect. : N.pairs= 687078 energy= -0.402E+04 vdWaals : N.pairs= 699117 energy= -0.443E+04
1-4 pairs H-bonds : N.pairs= 5 energy= -0.137 Elect. : N.pairs= 21311 energy= 0.430E+04 vdWaals : N.pairs= 21306 energy= 288.
Total H-bonds : N.pairs= 14521 energy= -861. Elect. : N.pairs= 708389 energy= 282. vdWaals : N.pairs= 720423 energy= -0.414E+04
Total non-bonded energy : -0.472E+04
On 11/27/2009 06:11 AM, leuven wrote: > When I get the models from modeller, there are always some atom clash�� > How to solve this problem?
You can certainly try to refine these models using the force field of your choice if you feel the clashes are too severe. Modeller includes the CHARMM forcefield so should tend to avoid generating clashes in the first place, but conflicts with other restraints (e.g. distance restraints from your templates) may interfere with this.
Ben Webb, Modeller Caretaker