Tue Oct 11 06:10:19 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+sph2.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 = amb2.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 06:10:19 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2023 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: 0.7141138 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): -9.5999956E-02 46.72300 ymin,ymax (A): 0.7880000 40.65500 zmin,zma (A): -3.881000 45.97100 x,y,z range (A): 46.81900 39.86700 49.85200 scale (grids/A): 0.7141138 object centre (A): 23.31350 20.72150 21.04500 number of atom coordinates read : 2023 total number of charged atoms : 1941 net assigned charge : 7.500009 assigned positive charge : 316.5971 centred at (gu) : 90.98330 90.06998 89.79872 assigned negative charge : -309.0971 centred at (gu) : 91.15581 90.04639 89.83141 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6780 nv = 96 ne = 84 npr = 41330 no. pairs analyzed = 41330 no. exposed pairs = 2374 no. arc points = 16227 no. surface atoms = 811 nbur = 1212 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 415 mr = 3874 m= 4 mr = 78 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 31 time to turn everything in is 0.2700000 number of dielectric boundary points 3247 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1597 ## 151 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7830 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.7166577E-08 5.4427876E-08 midg,1,midg; midg,igrid,midg 6.0861161E-08 8.9583551E-08 1,midg,midg; igrid,midg,midg 1.4183594E-07 -3.0865802E-08 gauss-seidel spectral radius is 0.9897661 estimated iterations to convergence 80 setup time was (sec) 0.5100000 now iterating at: 06:10:19 rms-change max change #iterations 0.2072153 28.29391 at 10iterations 2.6027607E-02 3.516144 at 20iterations 3.3075847E-03 0.4801235 at 30iterations 4.2083397E-04 6.4321518E-02 at 40iterations 5.5140306E-05 7.0343018E-03 at 50iterations finished qdiffx linear iterations at : 06:10:22 total time elapsed so far: 3.100000 # loops : 50 mean,max change (kT/e) : 5.5140306E-05 7.0343018E-03 energy calculations done at 3.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.280000 DelPhi exited at 06:10:22 3.286u 0.149s 0:03.75 91.2% 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 06:10:22 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2023 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: 2.142341 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): -9.5999956E-02 46.72300 ymin,ymax (A): 0.7880000 40.65500 zmin,zma (A): -3.881000 45.97100 x,y,z range (A): 46.81900 39.86700 49.85200 scale (grids/A): 2.142341 object centre (A): 23.31350 20.72150 21.04500 number of atom coordinates read : 2023 total number of charged atoms : 1941 net assigned charge : 7.500009 assigned positive charge : 316.5971 centred at (gu) : 92.94975 90.21001 89.39628 assigned negative charge : -309.0971 centred at (gu) : 93.46762 90.13935 89.49431 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 72043 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16227 grid for indexing accessible points = 1.400000 m= 27341 mr = 51147 m= 4987 mr = 20358 m= 516 mr = 3210 m= 14 mr = 288 m= 0 mr = 3 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 647 time to turn everything in is 0.5500000 number of dielectric boundary points 29895 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 63 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 15420 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) : 0.7141138 object centre at (A) : 23.31350 20.72150 21.04500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5663916E-02 6.4849816E-02 midg,1,midg; midg,igrid,midg 6.0017910E-03 2.9595878E-02 1,midg,midg; igrid,midg,midg 4.4088162E-02 1.7153593E-02 gauss-seidel spectral radius is 0.9988393 estimated iterations to convergence 232 setup time was (sec) 0.8400000 now iterating at: 06:10:23 rms-change max change #iterations 4.703458 197.7075 at 10iterations 2.336514 72.20573 at 20iterations 1.161790 39.08492 at 30iterations 0.5796984 19.44549 at 40iterations 0.2876428 8.889162 at 50iterations 0.1433819 4.581407 at 60iterations 7.1431011E-02 2.253777 at 70iterations 3.5502370E-02 1.059317 at 80iterations 1.7706061E-02 0.5275455 at 90iterations 8.7982630E-03 0.2764702 at 100iterations 4.3812990E-03 0.1461334 at 110iterations 2.1918197E-03 6.3623905E-02 at 120iterations finished qdiffx linear iterations at : 06:10:30 total time elapsed so far: 7.180000 # loops : 120 mean,max change (kT/e) : 2.1918197E-03 6.3623905E-02 energy calculations done at 7.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.370000 DelPhi exited at 06:10:30 7.369u 0.169s 0:07.94 94.7% 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 06:10:30 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2023 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: 3.213512 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): -9.5999956E-02 46.72300 ymin,ymax (A): 0.7880000 40.65500 zmin,zma (A): -3.881000 45.97100 x,y,z range (A): 46.81900 39.86700 49.85200 scale (grids/A): 3.213512 object centre (A): 23.31350 20.72150 21.04500 number of atom coordinates read : 2023 total number of charged atoms : 1941 net assigned charge : 7.500009 assigned positive charge : 316.5971 centred at (gu) : 94.42474 90.31509 89.09444 assigned negative charge : -309.0971 centred at (gu) : 95.20142 90.20902 89.24148 start vw surface at 0.1500000 fill in re-entrant regions at 0.8100000 boundary points on vw surface= 166343 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16227 grid for indexing accessible points = 1.400000 m= 86792 mr = 123160 m= 33487 mr = 71882 m= 9420 mr = 26996 m= 1935 mr = 7143 m= 260 mr = 1409 m= 15 mr = 174 m= 0 mr = 6 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 2027 time to turn everything in is 1.740000 number of dielectric boundary points 67482 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.880000 number of grid points assigned charge 15524 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) : 2.142341 object centre at (A) : 23.31350 20.72150 21.04500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2846121 0.7453040 midg,1,midg; midg,igrid,midg 3.0619824E-02 0.2269216 1,midg,midg; igrid,midg,midg 0.3451420 0.3070866 gauss-seidel spectral radius is 0.9992929 estimated iterations to convergence 297 setup time was (sec) 2.040000 now iterating at: 06:10:33 rms-change max change #iterations 10.41422 324.9531 at 10iterations 6.173371 138.8014 at 20iterations 3.637907 85.50564 at 30iterations 2.142124 46.68380 at 40iterations 1.255360 25.31179 at 50iterations 0.7387733 15.57523 at 60iterations 0.4319596 7.722150 at 70iterations 0.2534308 5.960227 at 80iterations 0.1480975 2.936251 at 90iterations 8.6657338E-02 1.651073 at 100iterations 5.0806656E-02 0.9896798 at 110iterations 2.9700316E-02 0.5381088 at 120iterations 1.7455880E-02 0.3437157 at 130iterations 1.0287867E-02 0.1792746 at 140iterations 6.1165770E-03 0.1089745 at 150iterations 3.6815670E-03 6.9068909E-02 at 160iterations 2.2736008E-03 4.4635773E-02 at 170iterations 1.4521321E-03 2.7503967E-02 at 180iterations finished qdiffx linear iterations at : 06:10:43 total time elapsed so far: 11.99000 # loops : 180 mean,max change (kT/e) : 1.4521321E-03 2.7503967E-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) 12.17000 DelPhi exited at 06:10:43 12.174u 0.177s 0:12.63 97.7% 0+0k 0+0io 0pf+0w