Mon Oct 10 13:59:51 PDT 2011 #!/bin/csh -f # input: # $1 receptor coordinates file; # $2 grid size; # $3 # of iterations for the first run; # $4 # of iterations for the second run; # $5 # of iterations for the third run; # output: # delphi map: $1.phi # log file: delphi.out set RECCRG = rec+sph2.crg set GRID = 179 set n1 = 50 set n2 = 120 set n3 = 180 set DELPHI = $DOCK_BASE/private/delphi set VDW = vdw.siz #set VDW = vdw.hydren set CRG = amb2.crg.oxt set PRM = genric.prm # three step focussing calc. if (-e ARCDAT) /bin/rm ARCDAT cp $VDW fort.11 cp $CRG fort.12 cp $RECCRG fort.13 echo "gsize=$GRID, perfil=20, bndcon=2, linit=$n1\n" >! fort.10 cat $PRM >> fort.10 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=60, bndcon=3, linit=$n2\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) echo "gsize=$GRID, perfil=90, bndcon=3, linit=$n3\n" >! fort.10 cat $PRM >> fort.10 mv fort.14 fort.18 time $DELPHI if ($status != 0) exit(100) /bin/rm fort.1[0-3] fort.18 ARCDAT mv fort.14 $RECCRG:r.phi ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 13:59:51 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3449 !!! WARNING: LLP 1 has a net charge of 1.1100 !!! WARNING: LLP 2 has a net charge of 0.4200 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5734074 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : dipolar x,y,z periodic bc. flags : F F F # of linear iterations : 50 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 20.00000 xmin,xmax (A): -11.22400 50.86100 ymin,ymax (A): -12.68400 42.40200 zmin,zma (A): 17.49200 75.75900 x,y,z range (A): 62.08500 55.08600 58.26701 scale (grids/A): 0.5734074 object centre (A): 19.81850 14.85900 46.62550 number of atom coordinates read : 3449 total number of charged atoms : 3296 net assigned charge : 5.030015 assigned positive charge : 535.7639 centred at (gu) : 90.94942 89.67858 88.15615 assigned negative charge : -530.7352 centred at (gu) : 90.84003 89.75172 88.13381 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7554 nv = 96 ne = 84 npr = 67200 no. pairs analyzed = 67200 no. exposed pairs = 4580 no. arc points = 32526 no. surface atoms = 1542 nbur = 1907 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 364 mr = 3764 m= 3 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 4120 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3227 ## 326 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 9514 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.6434768E-10 8.6036472E-10 midg,1,midg; midg,igrid,midg 2.5568421E-09 -6.4349076E-10 1,midg,midg; igrid,midg,midg -1.1676012E-09 3.9057251E-09 gauss-seidel spectral radius is 0.9843481 estimated iterations to convergence 66 setup time was (sec) 0.6400000 now iterating at: 13:59:52 rms-change max change #iterations 0.1003782 15.95525 at 10iterations 7.5518517E-03 1.259484 at 20iterations 5.8334728E-04 9.7887039E-02 at 30iterations 7.7250159E-05 1.3257027E-02 at 40iterations 3.5670819E-05 5.0325394E-03 at 50iterations finished qdiffx linear iterations at : 13:59:55 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 3.5670819E-05 5.0325394E-03 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.670000 DelPhi exited at 13:59:56 3.671u 0.207s 0:04.59 84.3% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 13:59:56 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3449 !!! WARNING: LLP 1 has a net charge of 1.1100 !!! WARNING: LLP 2 has a net charge of 0.4200 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.720222 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 120 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 60.00000 xmin,xmax (A): -11.22400 50.86100 ymin,ymax (A): -12.68400 42.40200 zmin,zma (A): 17.49200 75.75900 x,y,z range (A): 62.08500 55.08600 58.26701 scale (grids/A): 1.720222 object centre (A): 19.81850 14.85900 46.62550 number of atom coordinates read : 3449 total number of charged atoms : 3296 net assigned charge : 5.030015 assigned positive charge : 535.7639 centred at (gu) : 92.84756 89.03512 84.46796 assigned negative charge : -530.7352 centred at (gu) : 92.51986 89.25480 84.40086 start vw surface at 0.1900000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 82745 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32526 grid for indexing accessible points = 1.400000 m= 27560 mr = 55427 m= 3614 mr = 18670 m= 157 mr = 1857 m= 0 mr = 36 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 38086 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 337 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 25576 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 0.5734074 object centre at (A) : 19.81850 14.85900 46.62550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9334991E-02 7.8352541E-03 midg,1,midg; midg,igrid,midg 2.1579351E-02 -7.9206778E-03 1,midg,midg; igrid,midg,midg -1.1094382E-02 1.9872554E-03 gauss-seidel spectral radius is 0.9984239 estimated iterations to convergence 200 setup time was (sec) 0.9500000 now iterating at: 13:59:57 rms-change max change #iterations 4.207837 187.0294 at 10iterations 1.857744 64.69982 at 20iterations 0.8262078 30.13942 at 30iterations 0.3663209 11.73167 at 40iterations 0.1628875 5.434029 at 50iterations 7.2403789E-02 2.386939 at 60iterations 3.2095749E-02 1.070869 at 70iterations 1.4284818E-02 0.5038242 at 80iterations 6.3335509E-03 0.2200375 at 90iterations 2.8213253E-03 9.7134590E-02 at 100iterations 1.2548991E-03 4.2710304E-02 at 110iterations 5.6215038E-04 2.1903992E-02 at 120iterations finished qdiffx linear iterations at : 14:00:04 total time elapsed so far: 7.950000 # loops : 120 mean,max change (kT/e) : 5.6215038E-04 2.1903992E-02 energy calculations done at 7.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.170000 DelPhi exited at 14:00:07 8.175u 0.257s 0:10.94 76.9% 0+0k 0+0io 0pf+0w ___________________DelPhi II____________________ / | A program to solve the PB equation | | in 3D, using non-linear form, incorporating | | 2 dielectric regions, ionic strength, periodic | | and focussing boundary conditions, utilizing | | stripped optimum successive over-relaxation | | and an improved algorithm for mapping the | | Mol. Surface to the finite-Difference grid | __________________ ____________________/ DelPhi II program started on Mon Oct 10 2011 at 14:00:08 opening parameter file fort.10 atom radii read from file fort.11 ! default extended atom radii based loosely ! on mike connolly's MS program- note H's are 0 # of radius parameter records: 18 atomic charges read from file fort.12 # of charge parameter records: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3449 !!! WARNING: LLP 1 has a net charge of 1.1100 !!! WARNING: LLP 2 has a net charge of 0.4200 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.580333 object centred at (gu) : 0.0000000E+00 0.0000000E+00 0.0000000E+00 inner,outer dielectrics : 2.060000 78.50000 ionic strength (M) : 0.1450000 debye length (A) : 8.001814 ion exclusion radius (A) : 2.000000 probe radius (A) : 1.400000 boundary conditions : focussing x,y,z periodic bc. flags : F F F # of linear iterations : 180 # of non-linear iterations : 0 concentration map output : F spherical charge distbn. : F INSIGHT format output : F site potential output : F modified atom file output : T map file label : qdiffxas: qdiffxs4 with an improved surfacing routine convergence graph turned off potential listings turned off box fill (%): 90.00000 xmin,xmax (A): -11.22400 50.86100 ymin,ymax (A): -12.68400 42.40200 zmin,zma (A): 17.49200 75.75900 x,y,z range (A): 62.08500 55.08600 58.26701 scale (grids/A): 2.580333 object centre (A): 19.81850 14.85900 46.62550 number of atom coordinates read : 3449 total number of charged atoms : 3296 net assigned charge : 5.030015 assigned positive charge : 535.7639 centred at (gu) : 94.27104 88.55238 81.70168 assigned negative charge : -530.7352 centred at (gu) : 93.77966 88.88218 81.60132 start vw surface at 0.2000000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 191766 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32526 grid for indexing accessible points = 1.400000 m= 91626 mr = 135709 m= 29616 mr = 71584 m= 6039 mr = 22089 m= 648 mr = 4065 m= 19 mr = 378 m= 0 mr = 7 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.560000 number of dielectric boundary points 85882 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 26344 setting boundary conditions focussing boundary condition read from file fort.18 focussing potential map: qdiffxas: qdiffxs4 with an improved surfacing routine original scale (grids/A) : 1.720222 object centre at (A) : 19.81850 14.85900 46.62550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3474923 9.2748567E-02 midg,1,midg; midg,igrid,midg 0.3550287 -8.5562736E-02 1,midg,midg; igrid,midg,midg 9.5130075E-03 -0.4466587 gauss-seidel spectral radius is 0.9992282 estimated iterations to convergence 284 setup time was (sec) 1.910000 now iterating at: 14:00:10 rms-change max change #iterations 10.74339 395.6833 at 10iterations 6.368900 152.7001 at 20iterations 3.723404 87.98074 at 30iterations 2.167219 55.85535 at 40iterations 1.251701 26.42589 at 50iterations 0.7208329 13.54512 at 60iterations 0.4142135 9.520123 at 70iterations 0.2371746 4.746432 at 80iterations 0.1358033 2.664566 at 90iterations 7.7395111E-02 1.903605 at 100iterations 4.4291884E-02 0.8719482 at 110iterations 2.5247898E-02 0.4951143 at 120iterations 1.4406576E-02 0.2808075 at 130iterations 8.2164416E-03 0.1603624 at 140iterations 4.7055944E-03 8.8126659E-02 at 150iterations 2.6956857E-03 4.8820496E-02 at 160iterations 1.5657018E-03 3.1188965E-02 at 170iterations 9.3009608E-04 1.7420769E-02 at 180iterations finished qdiffx linear iterations at : 14:00:21 total time elapsed so far: 12.51000 # loops : 180 mean,max change (kT/e) : 9.3009608E-04 1.7420769E-02 energy calculations done at 12.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.70000 DelPhi exited at 14:00:22 12.703u 0.206s 0:13.60 94.8% 0+0k 0+0io 0pf+0w