Sun Oct 9 06:39:22 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 06:39:22 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 = 2015 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: 0.6587957 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): 2.874000 46.28200 ymin,ymax (A): 8.985001 54.72600 zmin,zma (A): 1.200000 55.23800 x,y,z range (A): 43.40800 45.74100 54.03800 scale (grids/A): 0.6587957 object centre (A): 24.57800 31.85550 28.21900 number of atom coordinates read : 2015 total number of charged atoms : 1874 net assigned charge : 2.500015 assigned positive charge : 299.1479 centred at (gu) : 89.05241 89.24148 88.71717 assigned negative charge : -296.6481 centred at (gu) : 89.00914 89.37836 88.63112 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5841 nv = 96 ne = 84 npr = 41030 no. pairs analyzed = 41030 no. exposed pairs = 2679 no. arc points = 18579 no. surface atoms = 899 nbur = 1116 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 334 mr = 3006 m= 0 mr = 42 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3127 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1765 ## 159 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6751 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.6330854E-09 1.4333935E-08 midg,1,midg; midg,igrid,midg 3.0453499E-08 -1.1932446E-08 1,midg,midg; igrid,midg,midg -2.3176544E-10 1.0309546E-08 gauss-seidel spectral radius is 0.9880065 estimated iterations to convergence 75 setup time was (sec) 0.4700000 now iterating at: 06:39:23 rms-change max change #iterations 0.1419819 26.14848 at 10iterations 1.4980095E-02 2.040657 at 20iterations 1.5693096E-03 0.2412992 at 30iterations 1.6479274E-04 2.5688171E-02 at 40iterations 1.7344766E-05 3.0364990E-03 at 50iterations finished qdiffx linear iterations at : 06:39:25 total time elapsed so far: 2.890000 # loops : 50 mean,max change (kT/e) : 1.7344766E-05 3.0364990E-03 energy calculations done at 2.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.060000 DelPhi exited at 06:39:25 3.060u 0.133s 0:03.48 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 Sun Oct 9 2011 at 06:39:26 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 = 2015 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: 1.976387 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): 2.874000 46.28200 ymin,ymax (A): 8.985001 54.72600 zmin,zma (A): 1.200000 55.23800 x,y,z range (A): 43.40800 45.74100 54.03800 scale (grids/A): 1.976387 object centre (A): 24.57800 31.85550 28.21900 number of atom coordinates read : 2015 total number of charged atoms : 1874 net assigned charge : 2.500015 assigned positive charge : 299.1479 centred at (gu) : 87.15731 87.72453 86.15157 assigned negative charge : -296.6481 centred at (gu) : 87.02740 88.13524 85.89337 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 61516 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18579 grid for indexing accessible points = 1.400000 m= 22427 mr = 40814 m= 3914 mr = 16254 m= 271 mr = 2428 m= 6 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 211 time to turn everything in is 0.4700000 number of dielectric boundary points 28540 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 89 iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 14809 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) : 0.6587957 object centre at (A) : 24.57800 31.85550 28.21900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.6709467E-02 -3.9665760E-03 midg,1,midg; midg,igrid,midg 2.3991430E-02 -1.3432727E-02 1,midg,midg; igrid,midg,midg 8.3464189E-03 2.9241491E-02 gauss-seidel spectral radius is 0.9986717 estimated iterations to convergence 217 setup time was (sec) 0.7400000 now iterating at: 06:39:26 rms-change max change #iterations 3.927144 209.0632 at 10iterations 1.849873 70.89151 at 20iterations 0.8725099 31.76033 at 30iterations 0.4105508 14.97263 at 40iterations 0.1946952 6.772770 at 50iterations 9.1670915E-02 2.907492 at 60iterations 4.3402661E-02 1.655917 at 70iterations 2.0509727E-02 0.8584290 at 80iterations 9.6832011E-03 0.3505707 at 90iterations 4.5776959E-03 0.1529694 at 100iterations 2.1588053E-03 7.2362900E-02 at 110iterations 1.0256417E-03 3.2183051E-02 at 120iterations finished qdiffx linear iterations at : 06:39:32 total time elapsed so far: 6.730000 # loops : 120 mean,max change (kT/e) : 1.0256417E-03 3.2183051E-02 energy calculations done at 6.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.890000 DelPhi exited at 06:39:33 6.892u 0.164s 0:07.33 96.1% 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 Sun Oct 9 2011 at 06:39:33 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 = 2015 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: 2.964581 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): 2.874000 46.28200 ymin,ymax (A): 8.985001 54.72600 zmin,zma (A): 1.200000 55.23800 x,y,z range (A): 43.40800 45.74100 54.03800 scale (grids/A): 2.964581 object centre (A): 24.57800 31.85550 28.21900 number of atom coordinates read : 2015 total number of charged atoms : 1874 net assigned charge : 2.500015 assigned positive charge : 299.1479 centred at (gu) : 85.73584 86.58679 84.22730 assigned negative charge : -296.6481 centred at (gu) : 85.54115 87.20291 83.84000 start vw surface at 0.1400000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 141550 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18579 grid for indexing accessible points = 1.400000 m= 70939 mr = 98860 m= 27250 mr = 57016 m= 7124 mr = 21730 m= 1121 mr = 5271 m= 104 mr = 723 m= 1 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 650 time to turn everything in is 1.120000 number of dielectric boundary points 64428 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.240000 number of grid points assigned charge 14988 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) : 1.976387 object centre at (A) : 24.57800 31.85550 28.21900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.8546361 -4.5230888E-02 midg,1,midg; midg,igrid,midg 0.2818257 -0.1156726 1,midg,midg; igrid,midg,midg 1.6747646E-02 0.3001639 gauss-seidel spectral radius is 0.9992639 estimated iterations to convergence 291 setup time was (sec) 1.390000 now iterating at: 06:39:34 rms-change max change #iterations 9.157854 356.5885 at 10iterations 5.290905 111.6777 at 20iterations 3.043083 63.78156 at 30iterations 1.759133 34.77924 at 40iterations 1.012519 19.59849 at 50iterations 0.5819165 11.51225 at 60iterations 0.3346775 6.528472 at 70iterations 0.1925056 3.919795 at 80iterations 0.1104535 2.233192 at 90iterations 6.3295394E-02 1.242821 at 100iterations 3.6432989E-02 0.8134689 at 110iterations 2.0880084E-02 0.4358187 at 120iterations 1.1993797E-02 0.2308788 at 130iterations 6.8777204E-03 0.1308823 at 140iterations 3.9581703E-03 7.5768471E-02 at 150iterations 2.2708119E-03 4.8904419E-02 at 160iterations 1.3042932E-03 2.5055885E-02 at 170iterations 7.4831716E-04 1.4545441E-02 at 180iterations finished qdiffx linear iterations at : 06:39:44 total time elapsed so far: 10.80000 # loops : 180 mean,max change (kT/e) : 7.4831716E-04 1.4545441E-02 energy calculations done at 10.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.97000 DelPhi exited at 06:39:44 10.974u 0.187s 0:11.43 97.5% 0+0k 0+0io 0pf+0w