Sat Oct 15 11:55:03 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 Sat Oct 15 2011 at 11:55:03 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 = 2226 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6491138 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): -13.87200 40.97200 ymin,ymax (A): -29.74900 24.09300 zmin,zma (A): -9.394000 34.80600 x,y,z range (A): 54.84400 53.84200 44.20000 scale (grids/A): 0.6491138 object centre (A): 13.55000 -2.828000 12.70600 number of atom coordinates read : 2226 total number of charged atoms : 2092 net assigned charge : 10.50002 assigned positive charge : 322.2318 centred at (gu) : 89.38603 91.29474 91.04109 assigned negative charge : -311.7322 centred at (gu) : 89.37234 91.28339 90.93983 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6595 nv = 96 ne = 84 npr = 43521 no. pairs analyzed = 43521 no. exposed pairs = 3134 no. arc points = 22176 no. surface atoms = 1034 nbur = 1192 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 412 mr = 3292 m= 3 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3657 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2151 ## 181 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7558 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.0888574E-09 3.9222552E-08 midg,1,midg; midg,igrid,midg 1.4046955E-08 2.7337235E-08 1,midg,midg; igrid,midg,midg 2.0332729E-08 1.8720714E-08 gauss-seidel spectral radius is 0.9876822 estimated iterations to convergence 74 setup time was (sec) 0.5600000 now iterating at: 11:55:04 rms-change max change #iterations 0.1338160 21.45448 at 10iterations 1.3883426E-02 2.008921 at 20iterations 1.3730807E-03 0.2074108 at 30iterations 1.4348094E-04 2.0812988E-02 at 40iterations 1.6360842E-05 2.4528503E-03 at 50iterations finished qdiffx linear iterations at : 11:55:08 total time elapsed so far: 3.960000 # loops : 50 mean,max change (kT/e) : 1.6360842E-05 2.4528503E-03 energy calculations done at 3.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.130000 DelPhi exited at 11:55:08 4.134u 0.339s 0:04.74 94.0% 0+0k 0+0io 6pf+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 Sat Oct 15 2011 at 11:55:08 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 = 2226 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.947341 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): -13.87200 40.97200 ymin,ymax (A): -29.74900 24.09300 zmin,zma (A): -9.394000 34.80600 x,y,z range (A): 54.84400 53.84200 44.20000 scale (grids/A): 1.947341 object centre (A): 13.55000 -2.828000 12.70600 number of atom coordinates read : 2226 total number of charged atoms : 2092 net assigned charge : 10.50002 assigned positive charge : 322.2318 centred at (gu) : 88.15800 93.88401 93.12337 assigned negative charge : -311.7322 centred at (gu) : 88.11716 93.85017 92.81973 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 69944 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22176 grid for indexing accessible points = 1.400000 m= 26014 mr = 45898 m= 4746 mr = 18567 m= 354 mr = 2942 m= 1 mr = 131 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 33521 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 124 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 16463 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) : 0.6491138 object centre at (A) : 13.55000 -2.828000 12.70600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.3308687E-03 2.6713887E-02 midg,1,midg; midg,igrid,midg 4.3981340E-02 3.0022146E-02 1,midg,midg; igrid,midg,midg 5.6367796E-02 4.5171238E-02 gauss-seidel spectral radius is 0.9986712 estimated iterations to convergence 217 setup time was (sec) 0.9300000 now iterating at: 11:55:10 rms-change max change #iterations 3.918899 223.4246 at 10iterations 1.843469 63.15051 at 20iterations 0.8706195 30.43544 at 30iterations 0.4126245 13.72551 at 40iterations 0.1937365 6.363141 at 50iterations 9.1615565E-02 3.330524 at 60iterations 4.3139886E-02 1.454229 at 70iterations 2.0452676E-02 0.6492329 at 80iterations 9.6371714E-03 0.3357811 at 90iterations 4.5435186E-03 0.1466370 at 100iterations 2.1535112E-03 7.6141357E-02 at 110iterations 1.0206756E-03 3.6003113E-02 at 120iterations finished qdiffx linear iterations at : 11:55:18 total time elapsed so far: 9.540000 # loops : 120 mean,max change (kT/e) : 1.0206756E-03 3.6003113E-02 energy calculations done at 9.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.730000 DelPhi exited at 11:55:19 9.731u 0.363s 0:10.39 97.1% 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 Sat Oct 15 2011 at 11:55:19 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 = 2226 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.921012 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): -13.87200 40.97200 ymin,ymax (A): -29.74900 24.09300 zmin,zma (A): -9.394000 34.80600 x,y,z range (A): 54.84400 53.84200 44.20000 scale (grids/A): 2.921012 object centre (A): 13.55000 -2.828000 12.70600 number of atom coordinates read : 2226 total number of charged atoms : 2092 net assigned charge : 10.50002 assigned positive charge : 322.2318 centred at (gu) : 87.23695 95.82590 94.68507 assigned negative charge : -311.7322 centred at (gu) : 87.17582 95.77537 94.22959 start vw surface at 0.1500000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 161209 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22176 grid for indexing accessible points = 1.400000 m= 81398 mr = 111646 m= 32132 mr = 64952 m= 8596 mr = 25470 m= 1487 mr = 6307 m= 112 mr = 973 m= 0 mr = 39 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.680000 number of dielectric boundary points 75547 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 16736 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) : 1.947341 object centre at (A) : 13.55000 -2.828000 12.70600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.6856945E-02 0.2430716 midg,1,midg; midg,igrid,midg 0.6739988 0.3008437 1,midg,midg; igrid,midg,midg 0.5557176 0.4407996 gauss-seidel spectral radius is 0.9992762 estimated iterations to convergence 293 setup time was (sec) 2.020000 now iterating at: 11:55:21 rms-change max change #iterations 9.339759 343.7805 at 10iterations 5.528150 174.8333 at 20iterations 3.249006 74.74679 at 30iterations 1.907523 43.95270 at 40iterations 1.113835 23.04115 at 50iterations 0.6477669 14.03639 at 60iterations 0.3779315 7.974774 at 70iterations 0.2194803 4.739914 at 80iterations 0.1271418 2.632309 at 90iterations 7.3751934E-02 1.437854 at 100iterations 4.2749822E-02 0.8227377 at 110iterations 2.4778208E-02 0.4562178 at 120iterations 1.4371909E-02 0.2942295 at 130iterations 8.3132163E-03 0.1570282 at 140iterations 4.8140069E-03 9.0188503E-02 at 150iterations 2.7804871E-03 5.0433159E-02 at 160iterations 1.6122902E-03 3.1057358E-02 at 170iterations 9.3343022E-04 1.7045498E-02 at 180iterations finished qdiffx linear iterations at : 11:55:35 total time elapsed so far: 16.30000 # loops : 180 mean,max change (kT/e) : 9.3343022E-04 1.7045498E-02 energy calculations done at 16.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.48000 DelPhi exited at 11:55:36 16.481u 0.334s 0:17.17 97.9% 0+0k 0+0io 0pf+0w