Sun Oct 9 13:42:26 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 13:42:26 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 = 2366 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: 0.6932949 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): -7.102000 44.24700 ymin,ymax (A): -14.17700 36.80900 zmin,zma (A): 1.038000 44.87000 x,y,z range (A): 51.34900 50.98600 43.83200 scale (grids/A): 0.6932949 object centre (A): 18.57250 11.31600 22.95400 number of atom coordinates read : 2366 total number of charged atoms : 2225 net assigned charge : 3.500020 assigned positive charge : 359.9891 centred at (gu) : 89.67307 91.28453 90.83463 assigned negative charge : -356.4896 centred at (gu) : 89.70104 91.43443 90.87883 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7763 nv = 96 ne = 84 npr = 47300 no. pairs analyzed = 47300 no. exposed pairs = 2916 no. arc points = 20397 no. surface atoms = 992 nbur = 1374 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 470 mr = 4346 m= 1 mr = 66 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 0.1800000 number of dielectric boundary points 3822 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1903 ## 178 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8696 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.3946502E-08 4.3627586E-09 midg,1,midg; midg,igrid,midg 6.3772013E-08 -5.2669641E-08 1,midg,midg; igrid,midg,midg 3.5621735E-08 9.9576862E-09 gauss-seidel spectral radius is 0.9891897 estimated iterations to convergence 78 setup time was (sec) 0.3600000 now iterating at: 13:42:27 rms-change max change #iterations 0.1936814 27.55252 at 10iterations 2.4233069E-02 3.337193 at 20iterations 3.4686804E-03 0.5107002 at 30iterations 8.1078062E-04 0.1115417 at 40iterations 2.6821220E-04 4.0283203E-02 at 50iterations finished qdiffx linear iterations at : 13:42:30 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 2.6821220E-04 4.0283203E-02 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 13:42:30 3.314u 0.178s 0:03.81 91.3% 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 Sun Oct 9 2011 at 13:42:30 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2366 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: 2.079885 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): -7.102000 44.24700 ymin,ymax (A): -14.17700 36.80900 zmin,zma (A): 1.038000 44.87000 x,y,z range (A): 51.34900 50.98600 43.83200 scale (grids/A): 2.079885 object centre (A): 18.57250 11.31600 22.95400 number of atom coordinates read : 2366 total number of charged atoms : 2225 net assigned charge : 3.500020 assigned positive charge : 359.9891 centred at (gu) : 89.01873 93.85301 92.50352 assigned negative charge : -356.4896 centred at (gu) : 89.10289 94.30315 92.63644 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 82464 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20397 grid for indexing accessible points = 1.400000 m= 31754 mr = 57860 m= 5460 mr = 23780 m= 491 mr = 3445 m= 11 mr = 265 m= 0 mr = 1 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 34829 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 102 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 17675 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) : 0.6932949 object centre at (A) : 18.57250 11.31600 22.95400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8268218E-02 8.2148071E-03 midg,1,midg; midg,igrid,midg 1.6163172E-02 -4.4280481E-02 1,midg,midg; igrid,midg,midg 5.5295032E-02 -1.3391180E-02 gauss-seidel spectral radius is 0.9988241 estimated iterations to convergence 231 setup time was (sec) 0.6200000 now iterating at: 13:42:31 rms-change max change #iterations 4.832611 199.0806 at 10iterations 2.379066 82.06221 at 20iterations 1.176162 36.31756 at 30iterations 0.5842481 20.28818 at 40iterations 0.2876802 9.487671 at 50iterations 0.1434272 3.981775 at 60iterations 7.1081541E-02 2.124954 at 70iterations 3.5491154E-02 1.073071 at 80iterations 1.7780116E-02 0.5494432 at 90iterations 9.0807751E-03 0.2606354 at 100iterations 4.7184713E-03 0.1500916 at 110iterations 2.5878530E-03 8.2101822E-02 at 120iterations finished qdiffx linear iterations at : 13:42:38 total time elapsed so far: 7.620000 # loops : 120 mean,max change (kT/e) : 2.5878530E-03 8.2101822E-02 energy calculations done at 7.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 13:42:38 7.752u 0.183s 0:08.26 96.0% 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 13:42:39 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 = 2366 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: 3.119827 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): -7.102000 44.24700 ymin,ymax (A): -14.17700 36.80900 zmin,zma (A): 1.038000 44.87000 x,y,z range (A): 51.34900 50.98600 43.83200 scale (grids/A): 3.119827 object centre (A): 18.57250 11.31600 22.95400 number of atom coordinates read : 2366 total number of charged atoms : 2225 net assigned charge : 3.500020 assigned positive charge : 359.9891 centred at (gu) : 88.52800 95.77930 93.75507 assigned negative charge : -356.4896 centred at (gu) : 88.65427 96.45457 93.95453 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 190552 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20397 grid for indexing accessible points = 1.400000 m= 100626 mr = 139958 m= 38456 mr = 83172 m= 10099 mr = 31113 m= 1980 mr = 7562 m= 240 mr = 1473 m= 3 mr = 148 m= 0 mr = 0 time to grow re-entrant surface = 0.6200001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.220000 number of dielectric boundary points 78530 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 17800 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) : 2.079885 object centre at (A) : 18.57250 11.31600 22.95400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4880749 -4.8694998E-02 midg,1,midg; midg,igrid,midg 0.2953747 -0.4822969 1,midg,midg; igrid,midg,midg 0.5280880 -0.4207384 gauss-seidel spectral radius is 0.9992970 estimated iterations to convergence 298 setup time was (sec) 1.450000 now iterating at: 13:42:40 rms-change max change #iterations 10.82823 442.7153 at 10iterations 6.425577 149.8668 at 20iterations 3.798596 70.42715 at 30iterations 2.244653 39.07694 at 40iterations 1.326094 22.44390 at 50iterations 0.7777094 13.43894 at 60iterations 0.4569010 7.537469 at 70iterations 0.2682329 5.205429 at 80iterations 0.1572874 2.557722 at 90iterations 9.2197940E-02 1.545212 at 100iterations 5.4193221E-02 1.003181 at 110iterations 3.2002594E-02 0.5176926 at 120iterations 1.9123387E-02 0.3481636 at 130iterations 1.1581951E-02 0.2116699 at 140iterations 7.3104962E-03 0.1533623 at 150iterations 4.8392718E-03 9.9922180E-02 at 160iterations 3.4086027E-03 6.8946838E-02 at 170iterations 2.5714876E-03 5.3401947E-02 at 180iterations finished qdiffx linear iterations at : 13:42:51 total time elapsed so far: 12.69000 # loops : 180 mean,max change (kT/e) : 2.5714876E-03 5.3401947E-02 energy calculations done at 12.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.82000 DelPhi exited at 13:42:52 12.820u 0.216s 0:13.31 97.8% 0+0k 0+0io 0pf+0w