Mon Oct 10 14:00:28 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 14:00:28 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 = 1962 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: 0.6410719 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): -3.832000 34.68500 ymin,ymax (A): -4.350000 49.20000 zmin,zma (A): -24.12200 31.41000 x,y,z range (A): 38.51700 53.55000 55.53200 scale (grids/A): 0.6410719 object centre (A): 15.42650 22.42500 3.644000 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 5.000007 assigned positive charge : 287.8260 centred at (gu) : 90.39858 92.59212 90.08878 assigned negative charge : -282.8263 centred at (gu) : 90.44196 92.64285 90.04361 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5598 nv = 96 ne = 84 npr = 39955 no. pairs analyzed = 39955 no. exposed pairs = 2491 no. arc points = 17449 no. surface atoms = 851 nbur = 1111 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 282 mr = 3120 m= 0 mr = 21 time to grow re-entrant surface = 9.9999979E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 2739 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1737 ## 155 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 6517 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.5909336E-09 1.1713938E-08 midg,1,midg; midg,igrid,midg 6.9970345E-09 5.2073310E-09 1,midg,midg; igrid,midg,midg 1.0433351E-08 4.1192347E-09 gauss-seidel spectral radius is 0.9873379 estimated iterations to convergence 73 setup time was (sec) 0.4900000 now iterating at: 14:00:29 rms-change max change #iterations 0.1224957 21.68721 at 10iterations 1.2216692E-02 2.149399 at 20iterations 1.1991860E-03 0.1964493 at 30iterations 1.2063583E-04 2.1461487E-02 at 40iterations 1.1885058E-05 1.8539429E-03 at 50iterations finished qdiffx linear iterations at : 14:00:31 total time elapsed so far: 3.130000 # loops : 50 mean,max change (kT/e) : 1.1885058E-05 1.8539429E-03 energy calculations done at 3.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 14:00:32 3.334u 0.153s 0:03.98 87.4% 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 14:00:32 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 = 1962 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: 1.923216 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): -3.832000 34.68500 ymin,ymax (A): -4.350000 49.20000 zmin,zma (A): -24.12200 31.41000 x,y,z range (A): 38.51700 53.55000 55.53200 scale (grids/A): 1.923216 object centre (A): 15.42650 22.42500 3.644000 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 5.000007 assigned positive charge : 287.8260 centred at (gu) : 91.19551 97.77647 90.26627 assigned negative charge : -282.8263 centred at (gu) : 91.32594 97.92879 90.13113 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 59737 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17449 grid for indexing accessible points = 1.400000 m= 22371 mr = 41260 m= 3235 mr = 17087 m= 142 mr = 2008 m= 2 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 834 time to turn everything in is 0.4800000 number of dielectric boundary points 25101 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 14434 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) : 0.6410719 object centre at (A) : 15.42650 22.42500 3.644000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.7560889E-02 2.0853290E-02 midg,1,midg; midg,igrid,midg 2.8913662E-02 1.0221791E-02 1,midg,midg; igrid,midg,midg 4.1048019E-03 5.6997756E-04 gauss-seidel spectral radius is 0.9985828 estimated iterations to convergence 211 setup time was (sec) 0.7800000 now iterating at: 14:00:33 rms-change max change #iterations 3.581602 159.4465 at 10iterations 1.650724 62.57710 at 20iterations 0.7634701 27.00605 at 30iterations 0.3526394 11.97455 at 40iterations 0.1629164 5.963148 at 50iterations 7.5217709E-02 3.016273 at 60iterations 3.4496728E-02 1.164324 at 70iterations 1.5941165E-02 0.5159531 at 80iterations 7.3530125E-03 0.2497709 at 90iterations 3.4021814E-03 0.1231499 at 100iterations 1.5691656E-03 6.0622334E-02 at 110iterations 7.2382909E-04 2.4682045E-02 at 120iterations finished qdiffx linear iterations at : 14:00:39 total time elapsed so far: 7.270000 # loops : 120 mean,max change (kT/e) : 7.2382909E-04 2.4682045E-02 energy calculations done at 7.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.510000 DelPhi exited at 14:00:40 7.511u 0.165s 0:08.11 94.5% 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 Mon Oct 10 2011 at 14:00:40 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 = 1962 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: 2.884823 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): -3.832000 34.68500 ymin,ymax (A): -4.350000 49.20000 zmin,zma (A): -24.12200 31.41000 x,y,z range (A): 38.51700 53.55000 55.53200 scale (grids/A): 2.884823 object centre (A): 15.42650 22.42500 3.644000 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 5.000007 assigned positive charge : 287.8260 centred at (gu) : 91.79333 101.6647 90.39940 assigned negative charge : -282.8263 centred at (gu) : 91.98906 101.8932 90.19683 start vw surface at 0.1600000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 137928 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17449 grid for indexing accessible points = 1.400000 m= 71659 mr = 99696 m= 26590 mr = 59603 m= 5686 mr = 22002 m= 605 mr = 4249 m= 25 mr = 337 m= 0 mr = 7 time to grow re-entrant surface = 0.6900001 no. cavity mid-points inaccessible to solvent = 3142 time to turn everything in is 1.210000 number of dielectric boundary points 56599 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 14640 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) : 1.923216 object centre at (A) : 15.42650 22.42500 3.644000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.065582 9.3231931E-02 midg,1,midg; midg,igrid,midg 0.2789206 5.0133206E-03 1,midg,midg; igrid,midg,midg 1.5766153E-02 9.9321045E-03 gauss-seidel spectral radius is 0.9992307 estimated iterations to convergence 285 setup time was (sec) 1.530000 now iterating at: 14:00:42 rms-change max change #iterations 8.542065 350.6430 at 10iterations 4.950508 151.5679 at 20iterations 2.837949 74.03880 at 30iterations 1.623919 53.71126 at 40iterations 0.9289692 18.73879 at 50iterations 0.5281978 11.89029 at 60iterations 0.3011109 6.085623 at 70iterations 0.1713708 3.736553 at 80iterations 9.7214729E-02 2.003380 at 90iterations 5.5423547E-02 1.195942 at 100iterations 3.1500440E-02 0.6038487 at 110iterations 1.7856706E-02 0.3443985 at 120iterations 1.0133674E-02 0.1890121 at 130iterations 5.7552187E-03 0.1102600 at 140iterations 3.2682447E-03 6.6463470E-02 at 150iterations 1.8550330E-03 3.4832001E-02 at 160iterations 1.0546579E-03 2.1751165E-02 at 170iterations 5.9875805E-04 1.3656616E-02 at 180iterations finished qdiffx linear iterations at : 14:00:52 total time elapsed so far: 11.99000 # loops : 180 mean,max change (kT/e) : 5.9875805E-04 1.3656616E-02 energy calculations done at 11.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.19000 DelPhi exited at 14:00:53 12.188u 0.205s 0:13.18 93.9% 0+0k 0+0io 0pf+0w