Tue Oct 11 07:51:01 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+sph.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 = amb.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 Tue Oct 11 2011 at 07:51:01 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2389 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6380386 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): -8.797000 36.58300 ymin,ymax (A): -14.82400 40.97200 zmin,zma (A): 5.365000 52.35700 x,y,z range (A): 45.38000 55.79600 46.99200 scale (grids/A): 0.6380386 object centre (A): 13.89300 13.07400 28.86100 number of atom coordinates read : 2389 total number of charged atoms : 2253 net assigned charge : 4.500007 assigned positive charge : 358.8513 centred at (gu) : 90.38844 88.66689 90.67432 assigned negative charge : -354.3517 centred at (gu) : 90.30600 88.66600 90.82245 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6480 nv = 96 ne = 84 npr = 48211 no. pairs analyzed = 48211 no. exposed pairs = 2848 no. arc points = 20049 no. surface atoms = 977 nbur = 1412 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 350 mr = 3598 m= 1 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3178 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2039 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7786 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8130189E-08 -1.0371953E-08 midg,1,midg; midg,igrid,midg 8.1654692E-09 4.8341406E-09 1,midg,midg; igrid,midg,midg -1.9085331E-09 1.5757271E-08 gauss-seidel spectral radius is 0.9872535 estimated iterations to convergence 72 setup time was (sec) 0.5000000 now iterating at: 07:51:02 rms-change max change #iterations 0.1385141 20.90182 at 10iterations 1.4016122E-02 2.120911 at 20iterations 1.5177225E-03 0.2737999 at 30iterations 2.1546369E-04 3.0742645E-02 at 40iterations 4.1290801E-05 6.7062378E-03 at 50iterations finished qdiffx linear iterations at : 07:51:05 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 4.1290801E-05 6.7062378E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 07:51:06 3.346u 0.197s 0:04.36 80.9% 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 Tue Oct 11 2011 at 07:51:06 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2389 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.914116 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): -8.797000 36.58300 ymin,ymax (A): -14.82400 40.97200 zmin,zma (A): 5.365000 52.35700 x,y,z range (A): 45.38000 55.79600 46.99200 scale (grids/A): 1.914116 object centre (A): 13.89300 13.07400 28.86100 number of atom coordinates read : 2389 total number of charged atoms : 2253 net assigned charge : 4.500007 assigned positive charge : 358.8513 centred at (gu) : 91.16475 86.00040 92.02283 assigned negative charge : -354.3517 centred at (gu) : 90.91788 85.99793 92.46717 start vw surface at 0.2000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 69422 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20049 grid for indexing accessible points = 1.400000 m= 26908 mr = 48375 m= 4411 mr = 20362 m= 267 mr = 2849 m= 3 mr = 93 m= 0 mr = 2 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6100000 number of dielectric boundary points 29330 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 140 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 17723 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) : 0.6380386 object centre at (A) : 13.89300 13.07400 28.86100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5645813E-02 -2.2755930E-02 midg,1,midg; midg,igrid,midg 8.4174471E-03 3.2973472E-02 1,midg,midg; igrid,midg,midg -2.4783313E-03 7.1702795E-03 gauss-seidel spectral radius is 0.9986258 estimated iterations to convergence 214 setup time was (sec) 0.8700000 now iterating at: 07:51:07 rms-change max change #iterations 4.069355 188.5600 at 10iterations 1.903138 71.83869 at 20iterations 0.8954914 31.99288 at 30iterations 0.4182412 13.51002 at 40iterations 0.1958240 6.213821 at 50iterations 9.1991827E-02 2.874542 at 60iterations 4.3044612E-02 1.355295 at 70iterations 2.0175431E-02 0.6910858 at 80iterations 9.4862487E-03 0.3028336 at 90iterations 4.4453428E-03 0.1413498 at 100iterations 2.1185374E-03 6.8611145E-02 at 110iterations 1.0101728E-03 3.0078888E-02 at 120iterations finished qdiffx linear iterations at : 07:51:13 total time elapsed so far: 7.480000 # loops : 120 mean,max change (kT/e) : 1.0101728E-03 3.0078888E-02 energy calculations done at 7.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.660000 DelPhi exited at 07:51:14 7.664u 0.183s 0:08.15 96.1% 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 Tue Oct 11 2011 at 07:51:14 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2389 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.871173 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): -8.797000 36.58300 ymin,ymax (A): -14.82400 40.97200 zmin,zma (A): 5.365000 52.35700 x,y,z range (A): 45.38000 55.79600 46.99200 scale (grids/A): 2.871173 object centre (A): 13.89300 13.07400 28.86100 number of atom coordinates read : 2389 total number of charged atoms : 2253 net assigned charge : 4.500007 assigned positive charge : 358.8513 centred at (gu) : 91.74703 84.00063 93.03414 assigned negative charge : -354.3517 centred at (gu) : 91.37679 83.99683 93.70065 start vw surface at 0.1500000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 160216 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20049 grid for indexing accessible points = 1.400000 m= 85077 mr = 116811 m= 33098 mr = 70463 m= 8020 mr = 27160 m= 1088 mr = 6185 m= 74 mr = 722 m= 0 mr = 25 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.270000 number of dielectric boundary points 66207 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 18015 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) : 1.914116 object centre at (A) : 13.89300 13.07400 28.86100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4064713 -0.3227786 midg,1,midg; midg,igrid,midg -0.1179470 0.3382284 1,midg,midg; igrid,midg,midg -9.2013786E-03 -1.0059642E-02 gauss-seidel spectral radius is 0.9992484 estimated iterations to convergence 288 setup time was (sec) 1.550000 now iterating at: 07:51:16 rms-change max change #iterations 9.535862 461.0759 at 10iterations 5.556624 132.1273 at 20iterations 3.222627 74.97858 at 30iterations 1.864043 39.95644 at 40iterations 1.074957 21.18285 at 50iterations 0.6177943 13.06892 at 60iterations 0.3552068 6.804531 at 70iterations 0.2039282 3.998856 at 80iterations 0.1169660 2.157771 at 90iterations 6.7127682E-02 1.231047 at 100iterations 3.8485028E-02 0.7389259 at 110iterations 2.2063835E-02 0.3846750 at 120iterations 1.2670572E-02 0.2360287 at 130iterations 7.2609116E-03 0.1381139 at 140iterations 4.1691530E-03 9.1035843E-02 at 150iterations 2.4102035E-03 4.1648865E-02 at 160iterations 1.4008234E-03 2.7002335E-02 at 170iterations 8.2425360E-04 1.5640259E-02 at 180iterations finished qdiffx linear iterations at : 07:51:26 total time elapsed so far: 11.86000 # loops : 180 mean,max change (kT/e) : 8.2425360E-04 1.5640259E-02 energy calculations done at 11.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.09000 DelPhi exited at 07:51:27 12.091u 0.204s 0:12.75 96.3% 0+0k 0+0io 0pf+0w