Sun Oct 9 17:26:37 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 Sun Oct 9 2011 at 17:26:37 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3656 !!! WARNING: HIR 571 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5608772 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): 3.450000 64.94500 ymin,ymax (A): 1.771000 61.82200 zmin,zma (A): -0.8310000 62.64100 x,y,z range (A): 61.49500 60.05100 63.47200 scale (grids/A): 0.5608772 object centre (A): 34.19750 31.79650 30.90500 number of atom coordinates read : 3656 total number of charged atoms : 3521 net assigned charge : -0.3649730 assigned positive charge : 555.4564 centred at (gu) : 89.64687 88.09678 88.49033 assigned negative charge : -555.8234 centred at (gu) : 89.58246 88.20233 88.39685 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7767 nv = 96 ne = 84 npr = 70443 no. pairs analyzed = 70443 no. exposed pairs = 4961 no. arc points = 34301 no. surface atoms = 1663 nbur = 1993 mkacc time = 0.1600000 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 = 1.540000 m= 369 mr = 3967 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 4151 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3528 ## 431 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 10027 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.0147104E-09 8.7719471E-10 midg,1,midg; midg,igrid,midg 2.3032531E-09 -9.8362796E-10 1,midg,midg; igrid,midg,midg -1.0528364E-09 7.9107987E-10 gauss-seidel spectral radius is 0.9836643 estimated iterations to convergence 64 setup time was (sec) 0.6100000 now iterating at: 17:26:38 rms-change max change #iterations 9.4313838E-02 16.15082 at 10iterations 7.4662473E-03 0.9744453 at 20iterations 1.7902616E-03 0.2187119 at 30iterations 1.0793942E-03 0.1252818 at 40iterations 6.7769276E-04 7.8947067E-02 at 50iterations finished qdiffx linear iterations at : 17:26:40 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 6.7769276E-04 7.8947067E-02 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 17:26:41 3.396u 0.156s 0:03.89 91.0% 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 17:26:41 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3656 !!! WARNING: HIR 571 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.682632 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): 3.450000 64.94500 ymin,ymax (A): 1.771000 61.82200 zmin,zma (A): -0.8310000 62.64100 x,y,z range (A): 61.49500 60.05100 63.47200 scale (grids/A): 1.682632 object centre (A): 34.19750 31.79650 30.90500 number of atom coordinates read : 3656 total number of charged atoms : 3521 net assigned charge : -0.3649730 assigned positive charge : 555.4564 centred at (gu) : 88.93958 84.28911 85.46953 assigned negative charge : -555.8234 centred at (gu) : 88.74698 84.60675 85.19024 start vw surface at 0.1800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 85531 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34301 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 29329 mr = 58259 m= 3830 mr = 20055 m= 135 mr = 1927 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6400000 number of dielectric boundary points 38573 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 325 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 27126 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) : 0.5608772 object centre at (A) : 34.19750 31.79650 30.90500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3200426E-02 -9.7253136E-03 midg,1,midg; midg,igrid,midg 1.4388117E-02 -7.1398034E-03 1,midg,midg; igrid,midg,midg 4.5328564E-03 1.2054406E-02 gauss-seidel spectral radius is 0.9983742 estimated iterations to convergence 197 setup time was (sec) 0.9300000 now iterating at: 17:26:42 rms-change max change #iterations 4.080730 186.1449 at 10iterations 1.784058 69.94773 at 20iterations 0.7818896 29.62762 at 30iterations 0.3420739 10.79546 at 40iterations 0.1498334 5.009444 at 50iterations 6.5830521E-02 2.137687 at 60iterations 2.9132763E-02 1.038132 at 70iterations 1.3043068E-02 0.3958282 at 80iterations 6.2455512E-03 0.2063007 at 90iterations 3.4864547E-03 0.1121140 at 100iterations 2.3858575E-03 6.9274902E-02 at 110iterations 1.8937386E-03 5.2310944E-02 at 120iterations finished qdiffx linear iterations at : 17:26:48 total time elapsed so far: 7.350000 # loops : 120 mean,max change (kT/e) : 1.8937386E-03 5.2310944E-02 energy calculations done at 7.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.540000 DelPhi exited at 17:26:49 7.541u 0.156s 0:07.97 96.4% 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 17:26:49 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3656 !!! WARNING: HIR 571 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.523947 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): 3.450000 64.94500 ymin,ymax (A): 1.771000 61.82200 zmin,zma (A): -0.8310000 62.64100 x,y,z range (A): 61.49500 60.05100 63.47200 scale (grids/A): 2.523947 object centre (A): 34.19750 31.79650 30.90500 number of atom coordinates read : 3656 total number of charged atoms : 3521 net assigned charge : -0.3649730 assigned positive charge : 555.4564 centred at (gu) : 88.40904 81.43342 83.20390 assigned negative charge : -555.8234 centred at (gu) : 88.12034 81.91001 82.78536 start vw surface at 0.1700000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 198163 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34301 grid for indexing accessible points = 1.400000 m= 97453 mr = 142451 m= 31782 mr = 76691 m= 6295 mr = 23670 m= 528 mr = 4115 m= 10 mr = 237 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.9399999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.560000 number of dielectric boundary points 87068 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.710000 number of grid points assigned charge 28145 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) : 1.682632 object centre at (A) : 34.19750 31.79650 30.90500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.7769511 -0.1708704 midg,1,midg; midg,igrid,midg 0.1940469 -9.8202877E-02 1,midg,midg; igrid,midg,midg 0.1195491 6.2496603E-02 gauss-seidel spectral radius is 0.9992210 estimated iterations to convergence 283 setup time was (sec) 1.870000 now iterating at: 17:26:51 rms-change max change #iterations 10.63985 399.6274 at 10iterations 6.308976 171.8648 at 20iterations 3.699975 80.93451 at 30iterations 2.148470 51.75259 at 40iterations 1.246977 27.43294 at 50iterations 0.7190962 14.46690 at 60iterations 0.4141231 8.460571 at 70iterations 0.2373620 5.029633 at 80iterations 0.1360428 3.042618 at 90iterations 7.7825285E-02 1.572369 at 100iterations 4.4457491E-02 0.8846588 at 110iterations 2.5334412E-02 0.4931641 at 120iterations 1.4465990E-02 0.2834778 at 130iterations 8.2521895E-03 0.1603737 at 140iterations 4.7097350E-03 8.8901520E-02 at 150iterations 2.6995528E-03 4.9629211E-02 at 160iterations 1.5697012E-03 3.3051491E-02 at 170iterations 9.3706866E-04 1.8852234E-02 at 180iterations finished qdiffx linear iterations at : 17:27:01 total time elapsed so far: 12.25000 # loops : 180 mean,max change (kT/e) : 9.3706866E-04 1.8852234E-02 energy calculations done at 12.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.44000 DelPhi exited at 17:27:02 12.445u 0.180s 0:12.91 97.7% 0+0k 0+0io 0pf+0w