Mon Oct 10 17:08:36 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 17:08:36 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2686 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: 0.5436608 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): -10.79000 48.32700 ymin,ymax (A): -7.086000 52.17100 zmin,zma (A): 25.53900 91.02100 x,y,z range (A): 59.11700 59.25700 65.48200 scale (grids/A): 0.5436608 object centre (A): 18.76850 22.54250 58.28000 number of atom coordinates read : 2686 total number of charged atoms : 2551 net assigned charge : 13.50002 assigned positive charge : 399.2545 centred at (gu) : 89.89156 89.48579 91.14800 assigned negative charge : -385.7554 centred at (gu) : 89.95116 89.35981 90.92628 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5413 nv = 96 ne = 84 npr = 49631 no. pairs analyzed = 49631 no. exposed pairs = 4087 no. arc points = 29316 no. surface atoms = 1356 nbur = 1330 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 216 mr = 2345 m= 3 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3280 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2891 ## 377 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 6903 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.2764561E-10 2.5246036E-09 midg,1,midg; midg,igrid,midg 8.6416069E-11 1.2441157E-09 1,midg,midg; igrid,midg,midg 1.0977860E-09 4.2862092E-10 gauss-seidel spectral radius is 0.9825547 estimated iterations to convergence 62 setup time was (sec) 0.6300000 now iterating at: 17:08:37 rms-change max change #iterations 6.5056823E-02 14.37370 at 10iterations 4.2055110E-03 0.7637634 at 20iterations 2.8027355E-04 4.4166565E-02 at 30iterations 2.3987812E-05 4.6234131E-03 at 40iterations 4.1332701E-06 1.0280609E-03 at 50iterations finished qdiffx linear iterations at : 17:08:41 total time elapsed so far: 4.600000 # loops : 50 mean,max change (kT/e) : 4.1332701E-06 1.0280609E-03 energy calculations done at 4.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.770000 DelPhi exited at 17:08:41 4.772u 0.369s 0:05.51 93.1% 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 Mon Oct 10 2011 at 17:08:41 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2686 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: 1.630983 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): -10.79000 48.32700 ymin,ymax (A): -7.086000 52.17100 zmin,zma (A): 25.53900 91.02100 x,y,z range (A): 59.11700 59.25700 65.48200 scale (grids/A): 1.630983 object centre (A): 18.76850 22.54250 58.28000 number of atom coordinates read : 2686 total number of charged atoms : 2551 net assigned charge : 13.50002 assigned positive charge : 399.2545 centred at (gu) : 89.67403 88.45660 93.44321 assigned negative charge : -385.7554 centred at (gu) : 89.85326 88.07922 92.77837 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 58488 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29316 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 18498 mr = 35913 m= 2196 mr = 11911 m= 81 mr = 976 m= 0 mr = 2 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 30461 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 342 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 19533 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) : 0.5436608 object centre at (A) : 18.76850 22.54250 58.28000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5053205E-02 2.4651030E-02 midg,1,midg; midg,igrid,midg 1.3120189E-02 1.9606117E-02 1,midg,midg; igrid,midg,midg 1.0133443E-02 3.2478368E-03 gauss-seidel spectral radius is 0.9981725 estimated iterations to convergence 186 setup time was (sec) 0.8300000 now iterating at: 17:08:43 rms-change max change #iterations 3.059491 154.6659 at 10iterations 1.254313 52.63551 at 20iterations 0.5207869 22.06405 at 30iterations 0.2144323 8.120790 at 40iterations 8.8605501E-02 3.216703 at 50iterations 3.6762662E-02 1.376163 at 60iterations 1.5257922E-02 0.5698013 at 70iterations 6.3055013E-03 0.2492924 at 80iterations 2.6175466E-03 0.1092567 at 90iterations 1.0936579E-03 4.1482925E-02 at 100iterations 4.5834272E-04 1.6662598E-02 at 110iterations 1.9610801E-04 7.6274872E-03 at 120iterations finished qdiffx linear iterations at : 17:08:52 total time elapsed so far: 10.55000 # loops : 120 mean,max change (kT/e) : 1.9610801E-04 7.6274872E-03 energy calculations done at 10.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.71000 DelPhi exited at 17:08:53 10.716u 0.417s 0:11.45 97.1% 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 Mon Oct 10 2011 at 17:08:53 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2686 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: 2.446474 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): -10.79000 48.32700 ymin,ymax (A): -7.086000 52.17100 zmin,zma (A): 25.53900 91.02100 x,y,z range (A): 59.11700 59.25700 65.48200 scale (grids/A): 2.446474 object centre (A): 18.76850 22.54250 58.28000 number of atom coordinates read : 2686 total number of charged atoms : 2551 net assigned charge : 13.50002 assigned positive charge : 399.2545 centred at (gu) : 89.51097 87.68468 95.16482 assigned negative charge : -385.7554 centred at (gu) : 89.77997 87.11874 94.16753 start vw surface at 0.1200000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 135234 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29316 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 61576 mr = 88664 m= 18738 mr = 46395 m= 3342 mr = 13366 m= 237 mr = 2015 m= 4 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.310000 number of dielectric boundary points 68633 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 20380 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) : 1.630983 object centre at (A) : 18.76850 22.54250 58.28000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4684866 0.4179109 midg,1,midg; midg,igrid,midg 0.1723314 0.2499605 1,midg,midg; igrid,midg,midg 0.1459040 5.9003472E-02 gauss-seidel spectral radius is 0.9991388 estimated iterations to convergence 269 setup time was (sec) 1.640000 now iterating at: 17:08:55 rms-change max change #iterations 8.130195 339.1478 at 10iterations 4.590291 126.8997 at 20iterations 2.568050 68.26366 at 30iterations 1.431164 34.23791 at 40iterations 0.7965910 18.46632 at 50iterations 0.4404602 10.18045 at 60iterations 0.2434700 5.948082 at 70iterations 0.1343718 3.178463 at 80iterations 7.3930472E-02 1.634439 at 90iterations 4.0711109E-02 0.8845969 at 100iterations 2.2408539E-02 0.4896784 at 110iterations 1.2330255E-02 0.2624216 at 120iterations 6.7890524E-03 0.1484394 at 130iterations 3.7325413E-03 8.4274292E-02 at 140iterations 2.0506564E-03 4.3105125E-02 at 150iterations 1.1316608E-03 2.5288224E-02 at 160iterations 6.2291522E-04 1.3162613E-02 at 170iterations 3.4646114E-04 8.2187653E-03 at 180iterations finished qdiffx linear iterations at : 17:09:12 total time elapsed so far: 18.16000 # loops : 180 mean,max change (kT/e) : 3.4646114E-04 8.2187653E-03 energy calculations done at 18.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.33000 DelPhi exited at 17:09:12 18.330u 0.454s 0:19.26 97.5% 0+0k 0+0io 0pf+0w