Sun Oct 9 21:18:10 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 Sun Oct 9 2011 at 21:18:10 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3026 !!! WARNING: SEP 141 has a net charge of -0.4750 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: 0.5880604 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): 2.057000 58.13300 ymin,ymax (A): 23.95500 84.49300 zmin,zma (A): -23.51700 28.94500 x,y,z range (A): 56.07600 60.53799 52.46200 scale (grids/A): 0.5880604 object centre (A): 30.09500 54.22400 2.714000 number of atom coordinates read : 3026 total number of charged atoms : 2975 net assigned charge : 4.025013 assigned positive charge : 474.7858 centred at (gu) : 88.67641 88.94315 90.55219 assigned negative charge : -470.7621 centred at (gu) : 88.63380 88.79834 90.55517 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7084 nv = 96 ne = 84 npr = 56435 no. pairs analyzed = 56435 no. exposed pairs = 4112 no. arc points = 30181 no. surface atoms = 1359 nbur = 1667 mkacc time = 0.1400000 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 = 1.456000 m= 315 mr = 3505 m= 0 mr = 35 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3859 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3124 ## 349 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9066 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1673834E-09 1.2914855E-09 midg,1,midg; midg,igrid,midg -4.1589567E-09 4.3343418E-09 1,midg,midg; igrid,midg,midg -1.1176091E-10 1.8578316E-09 gauss-seidel spectral radius is 0.9850875 estimated iterations to convergence 67 setup time was (sec) 0.5600000 now iterating at: 21:18:11 rms-change max change #iterations 0.1099958 17.20070 at 10iterations 8.5825901E-03 1.171871 at 20iterations 6.9817872E-04 0.1163120 at 30iterations 6.1309845E-05 9.2010498E-03 at 40iterations 7.9887359E-06 1.1138916E-03 at 50iterations finished qdiffx linear iterations at : 21:18:13 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 7.9887359E-06 1.1138916E-03 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 21:18:14 3.370u 0.145s 0:03.80 92.3% 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 Sun Oct 9 2011 at 21:18:14 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3026 !!! WARNING: SEP 141 has a net charge of -0.4750 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: 1.764181 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): 2.057000 58.13300 ymin,ymax (A): 23.95500 84.49300 zmin,zma (A): -23.51700 28.94500 x,y,z range (A): 56.07600 60.53799 52.46200 scale (grids/A): 1.764181 object centre (A): 30.09500 54.22400 2.714000 number of atom coordinates read : 3026 total number of charged atoms : 2975 net assigned charge : 4.025013 assigned positive charge : 474.7858 centred at (gu) : 86.02871 86.82875 91.65617 assigned negative charge : -470.7621 centred at (gu) : 85.90089 86.39479 91.66560 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 77220 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30181 grid for indexing accessible points = 1.400000 m= 24637 mr = 50721 m= 3219 mr = 16849 m= 133 mr = 1815 m= 2 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 710 time to turn everything in is 0.5600000 number of dielectric boundary points 35783 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 297 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 23098 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) : 0.5880604 object centre at (A) : 30.09500 54.22400 2.714000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0282126E-03 -2.4488585E-03 midg,1,midg; midg,igrid,midg -4.9543218E-03 2.0388305E-02 1,midg,midg; igrid,midg,midg 4.5697619E-03 -9.8599354E-03 gauss-seidel spectral radius is 0.9984782 estimated iterations to convergence 203 setup time was (sec) 0.8500000 now iterating at: 21:18:15 rms-change max change #iterations 4.050332 160.2936 at 10iterations 1.800408 67.33434 at 20iterations 0.8057667 27.96733 at 30iterations 0.3617966 11.59053 at 40iterations 0.1619656 5.970169 at 50iterations 7.2471358E-02 2.461642 at 60iterations 3.2445189E-02 1.074116 at 70iterations 1.4501569E-02 0.4675655 at 80iterations 6.5215053E-03 0.1988373 at 90iterations 2.9250702E-03 9.8155975E-02 at 100iterations 1.3116441E-03 4.0535927E-02 at 110iterations 5.9153058E-04 1.8963888E-02 at 120iterations finished qdiffx linear iterations at : 21:18:21 total time elapsed so far: 7.390000 # loops : 120 mean,max change (kT/e) : 5.9153058E-04 1.8963888E-02 energy calculations done at 7.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.590000 DelPhi exited at 21:18:22 7.591u 0.196s 0:08.14 95.5% 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 Sun Oct 9 2011 at 21:18:22 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3026 !!! WARNING: SEP 141 has a net charge of -0.4750 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: 2.646272 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): 2.057000 58.13300 ymin,ymax (A): 23.95500 84.49300 zmin,zma (A): -23.51700 28.94500 x,y,z range (A): 56.07600 60.53799 52.46200 scale (grids/A): 2.646272 object centre (A): 30.09500 54.22400 2.714000 number of atom coordinates read : 3026 total number of charged atoms : 2975 net assigned charge : 4.025013 assigned positive charge : 474.7858 centred at (gu) : 84.04287 85.24280 92.48404 assigned negative charge : -470.7621 centred at (gu) : 83.85126 84.59219 92.49808 start vw surface at 0.1600000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 178690 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30181 grid for indexing accessible points = 1.400000 m= 82922 mr = 124108 m= 26068 mr = 65015 m= 5422 mr = 19692 m= 630 mr = 3907 m= 17 mr = 387 m= 0 mr = 0 time to grow re-entrant surface = 0.8000000 no. cavity mid-points inaccessible to solvent = 2633 time to turn everything in is 1.380000 number of dielectric boundary points 80640 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 23789 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) : 1.764181 object centre at (A) : 30.09500 54.22400 2.714000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4519925E-02 -8.2006916E-02 midg,1,midg; midg,igrid,midg -0.1900291 0.2638628 1,midg,midg; igrid,midg,midg -8.7283552E-02 -0.2078602 gauss-seidel spectral radius is 0.9992423 estimated iterations to convergence 287 setup time was (sec) 1.680000 now iterating at: 21:18:24 rms-change max change #iterations 10.12305 344.7870 at 10iterations 5.961749 162.0864 at 20iterations 3.479876 82.48413 at 30iterations 2.026847 56.16827 at 40iterations 1.172444 24.26641 at 50iterations 0.6773551 16.27736 at 60iterations 0.3903249 9.214439 at 70iterations 0.2239953 4.838346 at 80iterations 0.1284860 2.724919 at 90iterations 7.3657781E-02 1.485231 at 100iterations 4.2230371E-02 0.8610806 at 110iterations 2.4207391E-02 0.4779434 at 120iterations 1.3820241E-02 0.2660375 at 130iterations 7.9049328E-03 0.1504070 at 140iterations 4.5291884E-03 8.6780548E-02 at 150iterations 2.5812008E-03 5.3155899E-02 at 160iterations 1.4753735E-03 2.8655291E-02 at 170iterations 8.4410497E-04 1.7954826E-02 at 180iterations finished qdiffx linear iterations at : 21:18:34 total time elapsed so far: 11.92000 # loops : 180 mean,max change (kT/e) : 8.4410497E-04 1.7954826E-02 energy calculations done at 11.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.13000 DelPhi exited at 21:18:35 12.129u 0.219s 0:12.66 97.3% 0+0k 0+0io 0pf+0w