Mon Oct 10 16:26:03 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 Mon Oct 10 2011 at 16:26:03 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 = 2423 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: 0.6151720 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): 207.5380 254.2130 ymin,ymax (A): 63.23200 109.3060 zmin,zma (A): 157.7240 215.5940 x,y,z range (A): 46.67499 46.07400 57.87000 scale (grids/A): 0.6151720 object centre (A): 230.8755 86.26900 186.6590 number of atom coordinates read : 2423 total number of charged atoms : 2283 net assigned charge : 10.00001 assigned positive charge : 364.3749 centred at (gu) : 89.44717 88.65768 90.67936 assigned negative charge : -354.3756 centred at (gu) : 89.58720 88.56586 90.74462 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6185 nv = 96 ne = 84 npr = 46959 no. pairs analyzed = 46959 no. exposed pairs = 3357 no. arc points = 23892 no. surface atoms = 1119 nbur = 1304 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 319 mr = 3051 m= 6 mr = 19 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 0.2900000 number of dielectric boundary points 3440 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2444 ## 278 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7597 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.9624654E-09 4.0512522E-09 midg,1,midg; midg,igrid,midg 2.7105003E-09 8.7837817E-09 1,midg,midg; igrid,midg,midg 1.6078090E-08 -3.9579912E-10 gauss-seidel spectral radius is 0.9863126 estimated iterations to convergence 70 setup time was (sec) 0.5400000 now iterating at: 16:26:04 rms-change max change #iterations 0.1158229 21.17824 at 10iterations 1.0293493E-02 1.776989 at 20iterations 9.1508572E-04 0.1481800 at 30iterations 8.3330648E-05 1.1876106E-02 at 40iterations 7.6498618E-06 1.1730194E-03 at 50iterations finished qdiffx linear iterations at : 16:26:07 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 7.6498618E-06 1.1730194E-03 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 16:26:07 3.549u 0.186s 0:04.18 88.9% 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 16:26:08 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2423 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: 1.845516 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): 207.5380 254.2130 ymin,ymax (A): 63.23200 109.3060 zmin,zma (A): 157.7240 215.5940 x,y,z range (A): 46.67499 46.07400 57.87000 scale (grids/A): 1.845516 object centre (A): 230.8755 86.26900 186.6590 number of atom coordinates read : 2423 total number of charged atoms : 2283 net assigned charge : 10.00001 assigned positive charge : 364.3749 centred at (gu) : 88.34096 85.97251 92.03770 assigned negative charge : -354.3756 centred at (gu) : 88.76144 85.69753 92.23369 start vw surface at 0.2200000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 66329 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23892 grid for indexing accessible points = 1.400000 m= 22854 mr = 42945 m= 3358 mr = 15943 m= 148 mr = 1846 m= 3 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5800000 number of dielectric boundary points 31927 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 189 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 17878 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) : 0.6151720 object centre at (A) : 230.8755 86.26900 186.6590 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.8299943E-03 3.1004196E-02 midg,1,midg; midg,igrid,midg -5.9938808E-03 1.1555225E-02 1,midg,midg; igrid,midg,midg 3.1202670E-02 1.2091631E-02 gauss-seidel spectral radius is 0.9985408 estimated iterations to convergence 208 setup time was (sec) 0.8600000 now iterating at: 16:26:09 rms-change max change #iterations 3.792813 168.2846 at 10iterations 1.719131 59.43202 at 20iterations 0.7849855 28.02851 at 30iterations 0.3569560 12.33584 at 40iterations 0.1629419 5.769220 at 50iterations 7.3962301E-02 2.682581 at 60iterations 3.3720136E-02 1.141806 at 70iterations 1.5315132E-02 0.5397925 at 80iterations 7.0103919E-03 0.2376259 at 90iterations 3.1917137E-03 0.1129456 at 100iterations 1.4588682E-03 5.2917480E-02 at 110iterations 6.6410628E-04 2.4200439E-02 at 120iterations finished qdiffx linear iterations at : 16:26:15 total time elapsed so far: 7.360000 # loops : 120 mean,max change (kT/e) : 6.6410628E-04 2.4200439E-02 energy calculations done at 7.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.540000 DelPhi exited at 16:26:16 7.543u 0.174s 0:08.14 94.7% 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 16:26:16 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 = 2423 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.768274 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): 207.5380 254.2130 ymin,ymax (A): 63.23200 109.3060 zmin,zma (A): 157.7240 215.5940 x,y,z range (A): 46.67499 46.07400 57.87000 scale (grids/A): 2.768274 object centre (A): 230.8755 86.26900 186.6590 number of atom coordinates read : 2423 total number of charged atoms : 2283 net assigned charge : 10.00001 assigned positive charge : 364.3749 centred at (gu) : 87.51143 83.95879 93.05637 assigned negative charge : -354.3756 centred at (gu) : 88.14211 83.54625 93.35049 start vw surface at 0.2100000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 153348 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23892 grid for indexing accessible points = 1.400000 m= 73919 mr = 105220 m= 25944 mr = 58092 m= 5792 mr = 19977 m= 731 mr = 3961 m= 23 mr = 405 m= 0 mr = 3 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.310000 number of dielectric boundary points 72099 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 18260 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) : 1.845516 object centre at (A) : 230.8755 86.26900 186.6590 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5666327 0.2736378 midg,1,midg; midg,igrid,midg -6.8048574E-02 0.1085311 1,midg,midg; igrid,midg,midg 0.2566212 0.1418007 gauss-seidel spectral radius is 0.9992399 estimated iterations to convergence 286 setup time was (sec) 1.640000 now iterating at: 16:26:18 rms-change max change #iterations 9.163909 300.4828 at 10iterations 5.366255 126.5314 at 20iterations 3.094889 78.74268 at 30iterations 1.783801 37.94864 at 40iterations 1.025108 23.62109 at 50iterations 0.5860235 12.01126 at 60iterations 0.3339384 6.767231 at 70iterations 0.1909552 3.861950 at 80iterations 0.1088722 2.152933 at 90iterations 6.2017132E-02 1.278790 at 100iterations 3.5333369E-02 0.6684533 at 110iterations 2.0173632E-02 0.4043045 at 120iterations 1.1473695E-02 0.2166786 at 130iterations 6.5434165E-03 0.1310577 at 140iterations 3.7173077E-03 7.6059341E-02 at 150iterations 2.1202876E-03 4.1336060E-02 at 160iterations 1.2040880E-03 2.3992062E-02 at 170iterations 6.8648357E-04 1.3763428E-02 at 180iterations finished qdiffx linear iterations at : 16:26:29 total time elapsed so far: 12.69000 # loops : 180 mean,max change (kT/e) : 6.8648357E-04 1.3763428E-02 energy calculations done at 12.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.89000 DelPhi exited at 16:26:29 12.890u 0.203s 0:13.68 95.6% 0+0k 0+0io 0pf+0w