Tue Oct 11 08:29:07 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 08:29:07 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 = 2836 !!! WARNING: ASP 287 has a net charge of -0.7280 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: 0.6246710 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): 10.26300 65.04600 ymin,ymax (A): -5.391000 47.54600 zmin,zma (A): -10.00100 46.98900 x,y,z range (A): 54.78300 52.93700 56.99000 scale (grids/A): 0.6246710 object centre (A): 37.65450 21.07750 18.49400 number of atom coordinates read : 2836 total number of charged atoms : 2687 net assigned charge : 4.772024 assigned positive charge : 429.1747 centred at (gu) : 91.76762 90.10538 90.95532 assigned negative charge : -424.4033 centred at (gu) : 91.52402 90.25337 90.96211 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7442 nv = 96 ne = 84 npr = 56735 no. pairs analyzed = 56735 no. exposed pairs = 3478 no. arc points = 24478 no. surface atoms = 1171 nbur = 1665 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 390 mr = 4127 m= 3 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.3600000 number of dielectric boundary points 3651 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2542 ## 282 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9066 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.7837489E-09 4.2764894E-09 midg,1,midg; midg,igrid,midg 1.5761916E-08 -8.6123526E-09 1,midg,midg; igrid,midg,midg -1.1226017E-08 3.5180566E-08 gauss-seidel spectral radius is 0.9867488 estimated iterations to convergence 71 setup time was (sec) 0.6300000 now iterating at: 08:29:07 rms-change max change #iterations 0.1356942 27.59238 at 10iterations 1.2837140E-02 1.612745 at 20iterations 1.3674106E-03 0.1736774 at 30iterations 2.0813488E-04 3.0246735E-02 at 40iterations 5.0123625E-05 8.8548660E-03 at 50iterations finished qdiffx linear iterations at : 08:29:11 total time elapsed so far: 3.890000 # loops : 50 mean,max change (kT/e) : 5.0123625E-05 8.8548660E-03 energy calculations done at 3.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.060000 DelPhi exited at 08:29:11 4.067u 0.269s 0:04.65 92.9% 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 08:29:11 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 = 2836 !!! WARNING: ASP 287 has a net charge of -0.7280 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: 1.874013 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): 10.26300 65.04600 ymin,ymax (A): -5.391000 47.54600 zmin,zma (A): -10.00100 46.98900 x,y,z range (A): 54.78300 52.93700 56.99000 scale (grids/A): 1.874013 object centre (A): 37.65450 21.07750 18.49400 number of atom coordinates read : 2836 total number of charged atoms : 2687 net assigned charge : 4.772024 assigned positive charge : 429.1747 centred at (gu) : 95.30266 90.31588 92.86548 assigned negative charge : -424.4033 centred at (gu) : 94.57190 90.75986 92.88618 start vw surface at 0.1600000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 80045 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24478 grid for indexing accessible points = 1.400000 m= 30136 mr = 55778 m= 4690 mr = 22675 m= 266 mr = 2974 m= 3 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 991 time to turn everything in is 0.7100000 number of dielectric boundary points 33627 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 194 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 21084 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) : 0.6246710 object centre at (A) : 37.65450 21.07750 18.49400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5482910E-02 -1.7327409E-02 midg,1,midg; midg,igrid,midg 2.5358707E-02 1.6888723E-04 1,midg,midg; igrid,midg,midg -4.0770327E-03 5.4533172E-02 gauss-seidel spectral radius is 0.9986185 estimated iterations to convergence 213 setup time was (sec) 1.010000 now iterating at: 08:29:13 rms-change max change #iterations 4.303111 182.9791 at 10iterations 2.001989 63.93964 at 20iterations 0.9348492 28.50926 at 30iterations 0.4385187 13.54004 at 40iterations 0.2032994 6.341452 at 50iterations 9.5116712E-02 2.859718 at 60iterations 4.4560377E-02 1.391707 at 70iterations 2.0808170E-02 0.5972958 at 80iterations 9.7507201E-03 0.2983303 at 90iterations 4.5591891E-03 0.1444368 at 100iterations 2.1585647E-03 6.4675093E-02 at 110iterations 1.0259534E-03 3.3267975E-02 at 120iterations finished qdiffx linear iterations at : 08:29:21 total time elapsed so far: 9.540000 # loops : 120 mean,max change (kT/e) : 1.0259534E-03 3.3267975E-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) 9.720000 DelPhi exited at 08:29:22 9.723u 0.287s 0:10.38 96.3% 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 08:29:22 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 = 2836 !!! WARNING: ASP 287 has a net charge of -0.7280 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: 2.811020 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): 10.26300 65.04600 ymin,ymax (A): -5.391000 47.54600 zmin,zma (A): -10.00100 46.98900 x,y,z range (A): 54.78300 52.93700 56.99000 scale (grids/A): 2.811020 object centre (A): 37.65450 21.07750 18.49400 number of atom coordinates read : 2836 total number of charged atoms : 2687 net assigned charge : 4.772024 assigned positive charge : 429.1747 centred at (gu) : 97.95380 90.47361 94.29806 assigned negative charge : -424.4033 centred at (gu) : 96.85767 91.13967 94.32906 start vw surface at 0.1600000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 185065 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24478 grid for indexing accessible points = 1.400000 m= 96811 mr = 134952 m= 35803 mr = 79840 m= 8415 mr = 29430 m= 1134 mr = 6341 m= 97 mr = 766 m= 0 mr = 42 time to grow re-entrant surface = 1.110000 no. cavity mid-points inaccessible to solvent = 3254 time to turn everything in is 1.830000 number of dielectric boundary points 75954 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.990000 number of grid points assigned charge 21494 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) : 1.874013 object centre at (A) : 37.65450 21.07750 18.49400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4118317 -0.3849222 midg,1,midg; midg,igrid,midg 0.2739247 8.5588150E-02 1,midg,midg; igrid,midg,midg -2.9574638E-02 0.5754182 gauss-seidel spectral radius is 0.9992592 estimated iterations to convergence 290 setup time was (sec) 2.160000 now iterating at: 08:29:24 rms-change max change #iterations 10.15648 372.4575 at 10iterations 5.956892 135.4241 at 20iterations 3.473528 79.31557 at 30iterations 2.015667 41.34377 at 40iterations 1.170015 24.76325 at 50iterations 0.6760570 13.61664 at 60iterations 0.3911882 6.988532 at 70iterations 0.2255441 4.161787 at 80iterations 0.1304266 2.432914 at 90iterations 7.5244308E-02 1.469238 at 100iterations 4.3392062E-02 0.8858194 at 110iterations 2.5049146E-02 0.4419689 at 120iterations 1.4490938E-02 0.2656212 at 130iterations 8.4012123E-03 0.1484756 at 140iterations 4.9139843E-03 9.5554352E-02 at 150iterations 2.9047136E-03 6.2322259E-02 at 160iterations 1.7496286E-03 3.1833649E-02 at 170iterations 1.0855481E-03 2.0675659E-02 at 180iterations finished qdiffx linear iterations at : 08:29:38 total time elapsed so far: 15.96000 # loops : 180 mean,max change (kT/e) : 1.0855481E-03 2.0675659E-02 energy calculations done at 15.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.14000 DelPhi exited at 08:29:38 16.140u 0.312s 0:16.76 98.1% 0+0k 0+0io 0pf+0w