Mon Oct 10 19:34:07 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+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 Mon Oct 10 2011 at 19:34:07 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2291 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: 0.7029461 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): -41.10200 4.341000 ymin,ymax (A): -23.75000 26.89400 zmin,zma (A): 32.49800 82.41300 x,y,z range (A): 45.44300 50.64400 49.91500 scale (grids/A): 0.7029461 object centre (A): -18.38050 1.572000 57.45550 number of atom coordinates read : 2291 total number of charged atoms : 2155 net assigned charge : 2.000004 assigned positive charge : 341.2971 centred at (gu) : 89.16512 87.49245 88.31786 assigned negative charge : -339.2977 centred at (gu) : 89.12621 87.63363 88.24177 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7618 nv = 96 ne = 84 npr = 47141 no. pairs analyzed = 47141 no. exposed pairs = 2820 no. arc points = 20204 no. surface atoms = 947 nbur = 1344 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 524 mr = 4243 m= 3 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 21 time to turn everything in is 0.3000000 number of dielectric boundary points 3838 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1825 ## 138 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8622 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.2603118E-08 3.6279282E-08 midg,1,midg; midg,igrid,midg 1.3434209E-07 -3.3140115E-08 1,midg,midg; igrid,midg,midg -5.8119549E-09 2.7790007E-08 gauss-seidel spectral radius is 0.9894785 estimated iterations to convergence 79 setup time was (sec) 0.5500000 now iterating at: 19:34:08 rms-change max change #iterations 0.2071649 31.55421 at 10iterations 2.5338130E-02 3.065141 at 20iterations 3.0424991E-03 0.3714318 at 30iterations 3.7265793E-04 4.6779633E-02 at 40iterations 4.5939116E-05 6.5660477E-03 at 50iterations finished qdiffx linear iterations at : 19:34:11 total time elapsed so far: 3.640000 # loops : 50 mean,max change (kT/e) : 4.5939116E-05 6.5660477E-03 energy calculations done at 3.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.830000 DelPhi exited at 19:34:11 3.833u 0.184s 0:04.44 90.3% 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 Mon Oct 10 2011 at 19:34:11 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2291 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: 2.108838 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): -41.10200 4.341000 ymin,ymax (A): -23.75000 26.89400 zmin,zma (A): 32.49800 82.41300 x,y,z range (A): 45.44300 50.64400 49.91500 scale (grids/A): 2.108838 object centre (A): -18.38050 1.572000 57.45550 number of atom coordinates read : 2291 total number of charged atoms : 2155 net assigned charge : 2.000004 assigned positive charge : 341.2971 centred at (gu) : 87.49476 82.47709 84.95303 assigned negative charge : -339.2977 centred at (gu) : 87.37836 82.90067 84.72505 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 80235 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20204 grid for indexing accessible points = 1.400000 m= 31670 mr = 55366 m= 6422 mr = 23687 m= 537 mr = 4184 m= 12 mr = 218 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1625 time to turn everything in is 0.6300000 number of dielectric boundary points 35421 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 57 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 17131 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) : 0.7029461 object centre at (A) : -18.38050 1.572000 57.45550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.1143101E-03 4.4364750E-02 midg,1,midg; midg,igrid,midg 5.1438592E-02 -1.8664328E-02 1,midg,midg; igrid,midg,midg 1.5057973E-02 1.4029422E-02 gauss-seidel spectral radius is 0.9988410 estimated iterations to convergence 232 setup time was (sec) 0.9300000 now iterating at: 19:34:12 rms-change max change #iterations 4.834934 209.4561 at 10iterations 2.397626 85.99686 at 20iterations 1.191035 42.07806 at 30iterations 0.5907155 16.11595 at 40iterations 0.2939568 8.037243 at 50iterations 0.1460733 4.259926 at 60iterations 7.2791621E-02 2.019697 at 70iterations 3.6030058E-02 1.061459 at 80iterations 1.8018559E-02 0.4991255 at 90iterations 8.9199981E-03 0.2539139 at 100iterations 4.4227736E-03 0.1546860 at 110iterations 2.2004924E-03 6.6349983E-02 at 120iterations finished qdiffx linear iterations at : 19:34:19 total time elapsed so far: 7.870000 # loops : 120 mean,max change (kT/e) : 2.2004924E-03 6.6349983E-02 energy calculations done at 7.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.060000 DelPhi exited at 19:34:20 8.064u 0.229s 0:08.76 94.5% 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 Mon Oct 10 2011 at 19:34:20 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2291 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: 3.163257 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): -41.10200 4.341000 ymin,ymax (A): -23.75000 26.89400 zmin,zma (A): 32.49800 82.41300 x,y,z range (A): 45.44300 50.64400 49.91500 scale (grids/A): 3.163257 object centre (A): -18.38050 1.572000 57.45550 number of atom coordinates read : 2291 total number of charged atoms : 2155 net assigned charge : 2.000004 assigned positive charge : 341.2971 centred at (gu) : 86.24204 78.71555 82.42957 assigned negative charge : -339.2977 centred at (gu) : 86.06754 79.35094 82.08766 start vw surface at 0.1500000 fill in re-entrant regions at 0.9200000 boundary points on vw surface= 185367 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20204 grid for indexing accessible points = 1.400000 m= 97079 mr = 133885 m= 40998 mr = 79799 m= 12063 mr = 33536 m= 2136 mr = 9212 m= 158 mr = 1409 m= 2 mr = 63 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 5469 time to turn everything in is 2.020000 number of dielectric boundary points 79899 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.160000 number of grid points assigned charge 17236 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) : 2.108838 object centre at (A) : -18.38050 1.572000 57.45550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.4187771E-04 0.8133662 midg,1,midg; midg,igrid,midg 0.4293636 -7.4145615E-02 1,midg,midg; igrid,midg,midg 0.2192360 3.1099334E-02 gauss-seidel spectral radius is 0.9993086 estimated iterations to convergence 300 setup time was (sec) 2.350000 now iterating at: 19:34:23 rms-change max change #iterations 10.93445 360.3895 at 10iterations 6.512863 175.8221 at 20iterations 3.856249 73.80722 at 30iterations 2.281172 73.10329 at 40iterations 1.348226 28.27419 at 50iterations 0.7935032 14.15762 at 60iterations 0.4669690 8.215878 at 70iterations 0.2742889 5.255836 at 80iterations 0.1608637 2.858389 at 90iterations 9.4612859E-02 1.642414 at 100iterations 5.5421002E-02 0.9383955 at 110iterations 3.2555614E-02 0.5328598 at 120iterations 1.9068163E-02 0.3185477 at 130iterations 1.1168160E-02 0.1870127 at 140iterations 6.5304739E-03 0.1055621 at 150iterations 3.8223607E-03 5.9820741E-02 at 160iterations 2.2439256E-03 3.4797668E-02 at 170iterations 1.3132032E-03 2.2500038E-02 at 180iterations finished qdiffx linear iterations at : 19:34:34 total time elapsed so far: 13.72000 # loops : 180 mean,max change (kT/e) : 1.3132032E-03 2.2500038E-02 energy calculations done at 13.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.92000 DelPhi exited at 19:34:35 13.917u 0.249s 0:14.77 95.8% 0+0k 0+0io 0pf+0w