Tue Oct 11 07:40:30 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 07:40:30 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2670 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6960874 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): -13.49600 37.64700 ymin,ymax (A): -22.60800 25.16700 zmin,zma (A): -5.856000 40.32000 x,y,z range (A): 51.14300 47.77500 46.17600 scale (grids/A): 0.6960874 object centre (A): 12.07550 1.279500 17.23200 number of atom coordinates read : 2670 total number of charged atoms : 2314 net assigned charge : 7.500009 assigned positive charge : 369.2081 centred at (gu) : 91.28239 88.76557 89.38493 assigned negative charge : -361.7086 centred at (gu) : 91.31306 88.77120 89.54310 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8076 nv = 96 ne = 84 npr = 49692 no. pairs analyzed = 49692 no. exposed pairs = 2940 no. arc points = 20244 no. surface atoms = 1006 nbur = 1664 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 488 mr = 4672 m= 1 mr = 80 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3813 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1840 ## 167 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 9076 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3162740E-07 -2.0211337E-08 midg,1,midg; midg,igrid,midg 6.3729473E-08 3.5861945E-08 1,midg,midg; igrid,midg,midg 4.7898702E-08 4.3440647E-08 gauss-seidel spectral radius is 0.9892802 estimated iterations to convergence 79 setup time was (sec) 0.3800000 now iterating at: 07:40:31 rms-change max change #iterations 0.2033505 34.67284 at 10iterations 2.4542062E-02 2.814531 at 20iterations 3.3216949E-03 0.4130554 at 30iterations 5.8417162E-04 7.7178955E-02 at 40iterations 1.4500278E-04 2.1938324E-02 at 50iterations finished qdiffx linear iterations at : 07:40:33 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.4500278E-04 2.1938324E-02 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 07:40:34 3.354u 0.178s 0:03.84 91.6% 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 07:40:34 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2670 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.088262 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): -13.49600 37.64700 ymin,ymax (A): -22.60800 25.16700 zmin,zma (A): -5.856000 40.32000 x,y,z range (A): 51.14300 47.77500 46.17600 scale (grids/A): 2.088262 object centre (A): 12.07550 1.279500 17.23200 number of atom coordinates read : 2670 total number of charged atoms : 2314 net assigned charge : 7.500009 assigned positive charge : 369.2081 centred at (gu) : 93.84677 86.29652 88.15442 assigned negative charge : -361.7086 centred at (gu) : 93.93907 86.31361 88.62914 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 85155 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20244 grid for indexing accessible points = 1.400000 m= 34333 mr = 60659 m= 6543 mr = 26444 m= 509 mr = 4404 m= 7 mr = 232 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 34809 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 85 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 18347 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) : 0.6960874 object centre at (A) : 12.07550 1.279500 17.23200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.3539421E-02 -9.1593862E-03 midg,1,midg; midg,igrid,midg 2.1145066E-02 2.6884777E-02 1,midg,midg; igrid,midg,midg 2.0377709E-02 5.0824683E-02 gauss-seidel spectral radius is 0.9988311 estimated iterations to convergence 232 setup time was (sec) 0.6400000 now iterating at: 07:40:35 rms-change max change #iterations 4.890812 227.9690 at 10iterations 2.425290 72.10795 at 20iterations 1.200899 36.71989 at 30iterations 0.5986166 20.55911 at 40iterations 0.2977537 8.765625 at 50iterations 0.1478160 5.128790 at 60iterations 7.3600546E-02 2.003750 at 70iterations 3.6747921E-02 1.039959 at 80iterations 1.8295845E-02 0.5193787 at 90iterations 9.1451565E-03 0.2778797 at 100iterations 4.5839823E-03 0.1332397 at 110iterations 2.3340026E-03 6.7304611E-02 at 120iterations finished qdiffx linear iterations at : 07:40:42 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 2.3340026E-03 6.7304611E-02 energy calculations done at 7.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.820000 DelPhi exited at 07:40:42 7.824u 0.197s 0:08.60 93.1% 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 Tue Oct 11 2011 at 07:40:42 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2670 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.132393 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): -13.49600 37.64700 ymin,ymax (A): -22.60800 25.16700 zmin,zma (A): -5.856000 40.32000 x,y,z range (A): 51.14300 47.77500 46.17600 scale (grids/A): 3.132393 object centre (A): 12.07550 1.279500 17.23200 number of atom coordinates read : 2670 total number of charged atoms : 2314 net assigned charge : 7.500009 assigned positive charge : 369.2081 centred at (gu) : 95.77014 84.44468 87.23160 assigned negative charge : -361.7086 centred at (gu) : 95.90852 84.47035 87.94371 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 196173 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20244 grid for indexing accessible points = 1.400000 m= 106834 mr = 145672 m= 44075 mr = 89787 m= 12259 mr = 36553 m= 2188 mr = 9529 m= 205 mr = 1546 m= 5 mr = 120 m= 0 mr = 0 time to grow re-entrant surface = 0.6799999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.310000 number of dielectric boundary points 78532 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 18508 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) : 2.088262 object centre at (A) : 12.07550 1.279500 17.23200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5361374 -0.1299370 midg,1,midg; midg,igrid,midg 0.1529568 0.2142631 1,midg,midg; igrid,midg,midg 5.4404858E-02 0.2651621 gauss-seidel spectral radius is 0.9992996 estimated iterations to convergence 298 setup time was (sec) 1.550000 now iterating at: 07:40:44 rms-change max change #iterations 10.77301 451.4501 at 10iterations 6.336598 154.3704 at 20iterations 3.714710 72.56327 at 30iterations 2.180577 39.82375 at 40iterations 1.277618 28.11075 at 50iterations 0.7479253 13.70392 at 60iterations 0.4365802 7.631155 at 70iterations 0.2556425 4.350986 at 80iterations 0.1494779 2.530703 at 90iterations 8.7320350E-02 1.482782 at 100iterations 5.1119074E-02 0.8217030 at 110iterations 2.9939987E-02 0.5591135 at 120iterations 1.7571976E-02 0.2827716 at 130iterations 1.0361602E-02 0.1610332 at 140iterations 6.1758207E-03 0.1083832 at 150iterations 3.7371982E-03 6.0379028E-02 at 160iterations 2.3272361E-03 4.0058136E-02 at 170iterations 1.5101738E-03 2.7137756E-02 at 180iterations finished qdiffx linear iterations at : 07:40:56 total time elapsed so far: 13.02000 # loops : 180 mean,max change (kT/e) : 1.5101738E-03 2.7137756E-02 energy calculations done at 13.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.16000 DelPhi exited at 07:40:56 13.157u 0.214s 0:13.97 95.6% 0+0k 0+0io 0pf+0w