Sun Oct 9 00:55:21 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 Sun Oct 9 2011 at 00:55:21 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 = 2331 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: 0.6614887 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): -0.5920000 53.22600 ymin,ymax (A): -16.20300 27.71800 zmin,zma (A): 32.33600 84.09700 x,y,z range (A): 53.81800 43.92100 51.76100 scale (grids/A): 0.6614887 object centre (A): 26.31700 5.757500 58.21650 number of atom coordinates read : 2331 total number of charged atoms : 2196 net assigned charge : 12.00002 assigned positive charge : 341.3453 centred at (gu) : 90.38312 89.62613 88.26182 assigned negative charge : -329.3461 centred at (gu) : 90.42876 89.65659 88.29316 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7010 nv = 96 ne = 84 npr = 46536 no. pairs analyzed = 46536 no. exposed pairs = 3076 no. arc points = 22289 no. surface atoms = 1034 nbur = 1297 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 444 mr = 3680 m= 4 mr = 68 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3710 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2076 ## 187 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8150 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.2734507E-08 1.8571185E-08 midg,1,midg; midg,igrid,midg 3.9734815E-08 2.4381036E-08 1,midg,midg; igrid,midg,midg 3.6521271E-08 2.5429879E-08 gauss-seidel spectral radius is 0.9881390 estimated iterations to convergence 75 setup time was (sec) 0.3600000 now iterating at: 00:55:21 rms-change max change #iterations 0.1523678 24.74599 at 10iterations 1.6269352E-02 2.190728 at 20iterations 2.0043114E-03 0.3344183 at 30iterations 4.4584309E-04 6.8918228E-02 at 40iterations 1.7156432E-04 2.5053978E-02 at 50iterations finished qdiffx linear iterations at : 00:55:24 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 1.7156432E-04 2.5053978E-02 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 00:55:25 3.460u 0.199s 0:03.93 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 Sun Oct 9 2011 at 00:55:25 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 = 2331 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: 1.984466 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): -0.5920000 53.22600 ymin,ymax (A): -16.20300 27.71800 zmin,zma (A): 32.33600 84.09700 x,y,z range (A): 53.81800 43.92100 51.76100 scale (grids/A): 1.984466 object centre (A): 26.31700 5.757500 58.21650 number of atom coordinates read : 2331 total number of charged atoms : 2196 net assigned charge : 12.00002 assigned positive charge : 341.3453 centred at (gu) : 91.14888 88.87803 84.78510 assigned negative charge : -329.3461 centred at (gu) : 91.28648 88.96967 84.87957 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 74732 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22289 grid for indexing accessible points = 1.400000 m= 27451 mr = 50310 m= 4935 mr = 19809 m= 383 mr = 3098 m= 16 mr = 145 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 152 time to turn everything in is 0.3800000 number of dielectric boundary points 34155 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 135 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 17368 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) : 0.6614887 object centre at (A) : 26.31700 5.757500 58.21650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9537117E-02 4.0992197E-02 midg,1,midg; midg,igrid,midg 2.9278936E-02 9.5048267E-03 1,midg,midg; igrid,midg,midg 6.3384727E-02 5.5848621E-02 gauss-seidel spectral radius is 0.9987218 estimated iterations to convergence 222 setup time was (sec) 0.6300000 now iterating at: 00:55:26 rms-change max change #iterations 4.203324 186.5555 at 10iterations 2.016520 73.26561 at 20iterations 0.9641452 29.00932 at 30iterations 0.4647634 14.38211 at 40iterations 0.2228250 6.976337 at 50iterations 0.1068113 3.883846 at 60iterations 5.1588237E-02 1.571867 at 70iterations 2.4685435E-02 0.7512875 at 80iterations 1.1896364E-02 0.3925438 at 90iterations 5.7703541E-03 0.1849442 at 100iterations 2.8669357E-03 8.8104248E-02 at 110iterations 1.4708783E-03 5.0632477E-02 at 120iterations finished qdiffx linear iterations at : 00:55:34 total time elapsed so far: 8.390000 # loops : 120 mean,max change (kT/e) : 1.4708783E-03 5.0632477E-02 energy calculations done at 8.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.550000 DelPhi exited at 00:55:34 8.555u 0.247s 0:09.08 96.8% 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 Sun Oct 9 2011 at 00:55:34 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2331 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: 2.976699 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): -0.5920000 53.22600 ymin,ymax (A): -16.20300 27.71800 zmin,zma (A): 32.33600 84.09700 x,y,z range (A): 53.81800 43.92100 51.76100 scale (grids/A): 2.976699 object centre (A): 26.31700 5.757500 58.21650 number of atom coordinates read : 2331 total number of charged atoms : 2196 net assigned charge : 12.00002 assigned positive charge : 341.3453 centred at (gu) : 91.72324 88.31695 82.17762 assigned negative charge : -329.3461 centred at (gu) : 91.92966 88.45454 82.31949 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 172525 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22289 grid for indexing accessible points = 1.400000 m= 87069 mr = 122264 m= 33382 mr = 70142 m= 9194 mr = 26488 m= 1587 mr = 6805 m= 139 mr = 1055 m= 8 mr = 79 m= 0 mr = 1 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 542 time to turn everything in is 1.000000 number of dielectric boundary points 77070 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 17568 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) : 1.984466 object centre at (A) : 26.31700 5.757500 58.21650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3828750 0.5700493 midg,1,midg; midg,igrid,midg 0.2670281 5.1711306E-02 1,midg,midg; igrid,midg,midg 0.5741376 0.5051681 gauss-seidel spectral radius is 0.9992878 estimated iterations to convergence 296 setup time was (sec) 1.260000 now iterating at: 00:55:36 rms-change max change #iterations 9.929413 484.5793 at 10iterations 5.911187 171.9341 at 20iterations 3.511003 97.20964 at 30iterations 2.073703 46.46935 at 40iterations 1.224117 30.29809 at 50iterations 0.7185027 14.26142 at 60iterations 0.4210973 8.534468 at 70iterations 0.2466971 5.113014 at 80iterations 0.1441076 2.996319 at 90iterations 8.4408700E-02 1.688227 at 100iterations 4.9141373E-02 1.008179 at 110iterations 2.8657194E-02 0.5591431 at 120iterations 1.6724147E-02 0.3297567 at 130iterations 9.7402092E-03 0.2012334 at 140iterations 5.6857355E-03 0.1095161 at 150iterations 3.3152513E-03 5.7621002E-02 at 160iterations 1.9435951E-03 3.8105011E-02 at 170iterations 1.1433223E-03 2.1848202E-02 at 180iterations finished qdiffx linear iterations at : 00:55:48 total time elapsed so far: 13.90000 # loops : 180 mean,max change (kT/e) : 1.1433223E-03 2.1848202E-02 energy calculations done at 13.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.03000 DelPhi exited at 00:55:49 14.032u 0.268s 0:14.62 97.7% 0+0k 0+0io 0pf+0w