Tue Oct 11 06:39:15 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 06:39:15 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 = 2065 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: 0.7115588 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): -20.20200 24.74800 ymin,ymax (A): -28.35900 11.05200 zmin,zma (A): -13.46000 36.57100 x,y,z range (A): 44.95000 39.41100 50.03100 scale (grids/A): 0.7115588 object centre (A): 2.273001 -8.653501 11.55550 number of atom coordinates read : 2065 total number of charged atoms : 1937 net assigned charge : 7.500009 assigned positive charge : 312.8170 centred at (gu) : 89.86860 90.63457 89.33453 assigned negative charge : -305.3172 centred at (gu) : 89.68413 90.60857 89.29104 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7053 nv = 96 ne = 84 npr = 41825 no. pairs analyzed = 41825 no. exposed pairs = 2479 no. arc points = 16791 no. surface atoms = 844 nbur = 1221 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 468 mr = 4094 m= 5 mr = 79 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 3353 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1609 ## 173 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7827 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2872117E-08 8.1959307E-08 midg,1,midg; midg,igrid,midg 5.0011497E-08 9.4451451E-08 1,midg,midg; igrid,midg,midg -3.0469547E-08 1.6181694E-07 gauss-seidel spectral radius is 0.9897001 estimated iterations to convergence 80 setup time was (sec) 0.5300000 now iterating at: 06:39:16 rms-change max change #iterations 0.2018154 26.65742 at 10iterations 2.5547195E-02 3.627785 at 20iterations 3.3621662E-03 0.4475517 at 30iterations 4.9671094E-04 7.7005386E-02 at 40iterations 1.0844243E-04 1.5823364E-02 at 50iterations finished qdiffx linear iterations at : 06:39:18 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 1.0844243E-04 1.5823364E-02 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 06:39:19 3.531u 0.184s 0:04.01 92.5% 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 Tue Oct 11 2011 at 06:39:19 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 = 2065 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: 2.134676 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): -20.20200 24.74800 ymin,ymax (A): -28.35900 11.05200 zmin,zma (A): -13.46000 36.57100 x,y,z range (A): 44.95000 39.41100 50.03100 scale (grids/A): 2.134676 object centre (A): 2.273001 -8.653501 11.55550 number of atom coordinates read : 2065 total number of charged atoms : 1937 net assigned charge : 7.500009 assigned positive charge : 312.8170 centred at (gu) : 89.60586 91.90366 88.00344 assigned negative charge : -305.3172 centred at (gu) : 89.05234 91.82593 87.87329 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 75025 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16791 grid for indexing accessible points = 1.400000 m= 29898 mr = 53733 m= 5850 mr = 22670 m= 543 mr = 3946 m= 9 mr = 267 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 30709 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 67 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 15389 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) : 0.7115588 object centre at (A) : 2.273001 -8.653501 11.55550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9764035E-02 4.6695929E-02 midg,1,midg; midg,igrid,midg 5.4165232E-03 3.7998606E-02 1,midg,midg; igrid,midg,midg 1.4436290E-02 4.4247061E-02 gauss-seidel spectral radius is 0.9988394 estimated iterations to convergence 232 setup time was (sec) 0.8900000 now iterating at: 06:39:20 rms-change max change #iterations 4.592793 220.9247 at 10iterations 2.279444 74.92928 at 20iterations 1.135617 35.86657 at 30iterations 0.5643588 17.70695 at 40iterations 0.2815721 9.015747 at 50iterations 0.1407401 4.237000 at 60iterations 6.9919579E-02 2.007143 at 70iterations 3.4895238E-02 1.131935 at 80iterations 1.7441241E-02 0.5645828 at 90iterations 8.7701865E-03 0.2526340 at 100iterations 4.3901294E-03 0.1203308 at 110iterations 2.2417651E-03 7.2624207E-02 at 120iterations finished qdiffx linear iterations at : 06:39:27 total time elapsed so far: 7.960000 # loops : 120 mean,max change (kT/e) : 2.2417651E-03 7.2624207E-02 energy calculations done at 7.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.160000 DelPhi exited at 06:39:28 8.158u 0.207s 0:08.99 92.8% 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 06:39:28 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 = 2065 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: 3.202015 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): -20.20200 24.74800 ymin,ymax (A): -28.35900 11.05200 zmin,zma (A): -13.46000 36.57100 x,y,z range (A): 44.95000 39.41100 50.03100 scale (grids/A): 3.202015 object centre (A): 2.273001 -8.653501 11.55550 number of atom coordinates read : 2065 total number of charged atoms : 1937 net assigned charge : 7.500009 assigned positive charge : 312.8170 centred at (gu) : 89.40891 92.85543 87.00513 assigned negative charge : -305.3172 centred at (gu) : 88.57859 92.73885 86.80991 start vw surface at 0.1600000 fill in re-entrant regions at 0.8500000 boundary points on vw surface= 173087 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16791 grid for indexing accessible points = 1.400000 m= 93344 mr = 129174 m= 37914 mr = 77797 m= 11262 mr = 31245 m= 2190 mr = 8822 m= 239 mr = 1582 m= 7 mr = 153 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.890000 number of dielectric boundary points 69269 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.020000 number of grid points assigned charge 15496 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) : 2.134676 object centre at (A) : 2.273001 -8.653501 11.55550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6334614 0.3865711 midg,1,midg; midg,igrid,midg 2.2088537E-02 0.3012705 1,midg,midg; igrid,midg,midg 0.2637289 0.3292328 gauss-seidel spectral radius is 0.9992931 estimated iterations to convergence 297 setup time was (sec) 2.210000 now iterating at: 06:39:30 rms-change max change #iterations 10.17142 314.5239 at 10iterations 6.021214 118.0190 at 20iterations 3.552570 86.26949 at 30iterations 2.094920 42.73315 at 40iterations 1.232550 23.12063 at 50iterations 0.7232192 15.30128 at 60iterations 0.4248533 9.092863 at 70iterations 0.2488572 4.221449 at 80iterations 0.1459725 3.000035 at 90iterations 8.5357301E-02 1.592338 at 100iterations 5.0120343E-02 0.9993505 at 110iterations 2.9461084E-02 0.5007011 at 120iterations 1.7364847E-02 0.3073196 at 130iterations 1.0349920E-02 0.1967907 at 140iterations 6.2790755E-03 0.1162338 at 150iterations 3.9260355E-03 7.2525024E-02 at 160iterations 2.5684957E-03 4.5806885E-02 at 170iterations 1.7804614E-03 3.2142639E-02 at 180iterations finished qdiffx linear iterations at : 06:39:42 total time elapsed so far: 14.28000 # loops : 180 mean,max change (kT/e) : 1.7804614E-03 3.2142639E-02 energy calculations done at 14.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.48000 DelPhi exited at 06:39:43 14.480u 0.220s 0:15.04 97.7% 0+0k 0+0io 0pf+0w