Mon Oct 10 14:03:06 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 14:03:07 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2139 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: 0.7199628 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): 13.66800 59.07500 ymin,ymax (A): 5.892000 48.88400 zmin,zma (A): -24.36100 25.08600 x,y,z range (A): 45.40700 42.99200 49.44700 scale (grids/A): 0.7199628 object centre (A): 36.37150 27.38800 0.3625002 number of atom coordinates read : 2139 total number of charged atoms : 1999 net assigned charge : -5.999979 assigned positive charge : 322.3839 centred at (gu) : 89.34518 91.58356 91.05785 assigned negative charge : -328.3840 centred at (gu) : 89.48954 91.44707 90.87910 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7448 nv = 96 ne = 84 npr = 44659 no. pairs analyzed = 44659 no. exposed pairs = 2667 no. arc points = 18962 no. surface atoms = 899 nbur = 1240 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 447 mr = 4074 m= 1 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 32 time to turn everything in is 0.2900000 number of dielectric boundary points 3750 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1588 ## 145 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8156 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5946452E-07 6.1348779E-08 midg,1,midg; midg,igrid,midg -1.2248238E-07 3.0421202E-08 1,midg,midg; igrid,midg,midg 3.0376473E-08 -1.5088011E-07 gauss-seidel spectral radius is 0.9899514 estimated iterations to convergence 81 setup time was (sec) 0.5300000 now iterating at: 14:03:07 rms-change max change #iterations 0.2239504 26.92627 at 10iterations 2.8627042E-02 4.295952 at 20iterations 3.6384990E-03 0.5243607 at 30iterations 4.6444443E-04 6.3264847E-02 at 40iterations 5.9550985E-05 8.6450577E-03 at 50iterations finished qdiffx linear iterations at : 14:03:10 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 5.9550985E-05 8.6450577E-03 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 14:03:11 3.551u 0.218s 0:04.10 91.7% 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 Mon Oct 10 2011 at 14:03:11 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2139 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.159889 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): 13.66800 59.07500 ymin,ymax (A): 5.892000 48.88400 zmin,zma (A): -24.36100 25.08600 x,y,z range (A): 45.40700 42.99200 49.44700 scale (grids/A): 2.159889 object centre (A): 36.37150 27.38800 0.3625002 number of atom coordinates read : 2139 total number of charged atoms : 1999 net assigned charge : -5.999979 assigned positive charge : 322.3839 centred at (gu) : 88.03535 94.75043 93.17361 assigned negative charge : -328.3840 centred at (gu) : 88.46873 94.34131 92.63746 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 78496 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18962 grid for indexing accessible points = 1.400000 m= 29957 mr = 53742 m= 5873 mr = 22426 m= 579 mr = 3974 m= 17 mr = 298 m= 0 mr = 2 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 795 time to turn everything in is 0.6400000 number of dielectric boundary points 34480 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 58 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 15922 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) : 0.7199628 object centre at (A) : 36.37150 27.38800 0.3625002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.9922679E-02 -2.8580146E-02 midg,1,midg; midg,igrid,midg -3.6252763E-02 -2.9866178E-02 1,midg,midg; igrid,midg,midg 2.7705273E-02 -1.0956174E-02 gauss-seidel spectral radius is 0.9988745 estimated iterations to convergence 236 setup time was (sec) 0.9600000 now iterating at: 14:03:12 rms-change max change #iterations 4.902188 192.0367 at 10iterations 2.446304 80.32493 at 20iterations 1.228706 37.29527 at 30iterations 0.6144713 19.22892 at 40iterations 0.3085021 8.946358 at 50iterations 0.1547127 4.541047 at 60iterations 7.7492185E-02 2.327743 at 70iterations 3.8927570E-02 1.173059 at 80iterations 1.9569319E-02 0.5271015 at 90iterations 9.8274369E-03 0.2756042 at 100iterations 4.9324632E-03 0.1387062 at 110iterations 2.4676730E-03 7.4329376E-02 at 120iterations finished qdiffx linear iterations at : 14:03:19 total time elapsed so far: 8.100000 # loops : 120 mean,max change (kT/e) : 2.4676730E-03 7.4329376E-02 energy calculations done at 8.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.290000 DelPhi exited at 14:03:20 8.290u 0.217s 0:08.86 95.9% 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 14:03:20 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2139 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: 3.239833 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): 13.66800 59.07500 ymin,ymax (A): 5.892000 48.88400 zmin,zma (A): -24.36100 25.08600 x,y,z range (A): 45.40700 42.99200 49.44700 scale (grids/A): 3.239833 object centre (A): 36.37150 27.38800 0.3625002 number of atom coordinates read : 2139 total number of charged atoms : 1999 net assigned charge : -5.999979 assigned positive charge : 322.3839 centred at (gu) : 87.05317 97.12554 94.76041 assigned negative charge : -328.3840 centred at (gu) : 87.70304 96.51195 93.95615 start vw surface at 0.1600000 fill in re-entrant regions at 0.9200000 boundary points on vw surface= 180839 reading accessible surface arcs data from file ARCDAT no. of arc points read = 18962 grid for indexing accessible points = 1.400000 m= 93188 mr = 129595 m= 37684 mr = 76779 m= 11259 mr = 30794 m= 2425 mr = 8779 m= 314 mr = 1833 m= 14 mr = 197 m= 0 mr = 1 time to grow re-entrant surface = 0.9300001 no. cavity mid-points inaccessible to solvent = 2744 time to turn everything in is 1.980000 number of dielectric boundary points 77745 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.120000 number of grid points assigned charge 15992 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) : 2.159889 object centre at (A) : 36.37150 27.38800 0.3625002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.8137939 -0.3143524 midg,1,midg; midg,igrid,midg -0.2365481 -0.2772526 1,midg,midg; igrid,midg,midg 0.1611203 -6.2874392E-02 gauss-seidel spectral radius is 0.9993082 estimated iterations to convergence 300 setup time was (sec) 2.310000 now iterating at: 14:03:22 rms-change max change #iterations 10.78419 329.8578 at 10iterations 6.327392 131.8116 at 20iterations 3.717238 67.04044 at 30iterations 2.175229 52.28208 at 40iterations 1.273052 24.20356 at 50iterations 0.7468496 13.60912 at 60iterations 0.4366398 7.232395 at 70iterations 0.2550530 4.316705 at 80iterations 0.1490294 2.747749 at 90iterations 8.7016724E-02 1.386612 at 100iterations 5.0979543E-02 1.069824 at 110iterations 2.9821320E-02 0.5183907 at 120iterations 1.7467894E-02 0.2780409 at 130iterations 1.0184405E-02 0.1824064 at 140iterations 5.9582451E-03 9.8183155E-02 at 150iterations 3.4837576E-03 5.4672241E-02 at 160iterations 2.0382493E-03 3.1787992E-02 at 170iterations 1.1928371E-03 2.0494819E-02 at 180iterations finished qdiffx linear iterations at : 14:03:34 total time elapsed so far: 14.01000 # loops : 180 mean,max change (kT/e) : 1.1928371E-03 2.0494819E-02 energy calculations done at 14.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.19000 DelPhi exited at 14:03:35 14.190u 0.265s 0:15.29 94.5% 0+0k 0+0io 0pf+0w