Sun Oct 9 13:51:48 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 13:51:48 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 = 2375 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: 0.7002912 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): -18.41200 30.73100 ymin,ymax (A): -20.55100 30.28500 zmin,zma (A): 4.184000 48.36000 x,y,z range (A): 49.14300 50.83600 44.17600 scale (grids/A): 0.7002912 object centre (A): 6.159501 4.867000 26.27200 number of atom coordinates read : 2375 total number of charged atoms : 2234 net assigned charge : 3.500020 assigned positive charge : 361.0370 centred at (gu) : 90.59311 90.09450 90.29034 assigned negative charge : -357.5376 centred at (gu) : 90.75997 90.17297 90.36880 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8006 nv = 96 ne = 84 npr = 47631 no. pairs analyzed = 47631 no. exposed pairs = 2994 no. arc points = 20924 no. surface atoms = 1010 nbur = 1365 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 466 mr = 4448 m= 3 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.2900000 number of dielectric boundary points 3955 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1937 ## 182 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8823 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.9733310E-08 -1.3284060E-08 midg,1,midg; midg,igrid,midg 6.2075159E-08 -1.2708704E-08 1,midg,midg; igrid,midg,midg 9.3217750E-08 -6.3502362E-08 gauss-seidel spectral radius is 0.9894069 estimated iterations to convergence 79 setup time was (sec) 0.5000000 now iterating at: 13:51:49 rms-change max change #iterations 0.2068864 27.58788 at 10iterations 2.5252828E-02 3.347123 at 20iterations 3.5558352E-03 0.4790001 at 30iterations 7.8685069E-04 0.1179810 at 40iterations 2.5395709E-04 4.0508270E-02 at 50iterations finished qdiffx linear iterations at : 13:51:51 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 2.5395709E-04 4.0508270E-02 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 13:51:52 3.090u 0.136s 0:03.51 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 Sun Oct 9 2011 at 13:51:52 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 = 2375 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: 2.100873 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): -18.41200 30.73100 ymin,ymax (A): -20.55100 30.28500 zmin,zma (A): 4.184000 48.36000 x,y,z range (A): 49.14300 50.83600 44.17600 scale (grids/A): 2.100873 object centre (A): 6.159501 4.867000 26.27200 number of atom coordinates read : 2375 total number of charged atoms : 2234 net assigned charge : 3.500020 assigned positive charge : 361.0370 centred at (gu) : 91.77885 90.28292 90.87052 assigned negative charge : -357.5376 centred at (gu) : 92.27961 90.51865 91.10629 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 84832 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20924 grid for indexing accessible points = 1.400000 m= 32347 mr = 59179 m= 5712 mr = 24098 m= 481 mr = 3654 m= 12 mr = 212 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 300 time to turn everything in is 0.5900000 number of dielectric boundary points 36241 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 103 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 17761 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) : 0.7002912 object centre at (A) : 6.159501 4.867000 26.27200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.7361506E-02 8.4473081E-03 midg,1,midg; midg,igrid,midg -6.2212028E-04 -4.0066849E-02 1,midg,midg; igrid,midg,midg 5.9999141E-04 -4.6463177E-02 gauss-seidel spectral radius is 0.9988500 estimated iterations to convergence 233 setup time was (sec) 0.8500000 now iterating at: 13:51:53 rms-change max change #iterations 4.939254 214.7712 at 10iterations 2.443595 82.97530 at 20iterations 1.216537 35.48173 at 30iterations 0.6071638 18.78705 at 40iterations 0.3029137 8.714640 at 50iterations 0.1514591 4.325009 at 60iterations 7.5623162E-02 2.127301 at 70iterations 3.7909899E-02 1.066497 at 80iterations 1.9035680E-02 0.5670004 at 90iterations 9.6610514E-03 0.2679520 at 100iterations 4.9722195E-03 0.1435699 at 110iterations 2.6380459E-03 7.8353882E-02 at 120iterations finished qdiffx linear iterations at : 13:51:59 total time elapsed so far: 6.850000 # loops : 120 mean,max change (kT/e) : 2.6380459E-03 7.8353882E-02 energy calculations done at 6.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.020000 DelPhi exited at 13:51:59 7.028u 0.155s 0:07.46 96.1% 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 Sun Oct 9 2011 at 13:51:59 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 = 2375 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: 3.151310 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): -18.41200 30.73100 ymin,ymax (A): -20.55100 30.28500 zmin,zma (A): 4.184000 48.36000 x,y,z range (A): 49.14300 50.83600 44.17600 scale (grids/A): 3.151310 object centre (A): 6.159501 4.867000 26.27200 number of atom coordinates read : 2375 total number of charged atoms : 2234 net assigned charge : 3.500020 assigned positive charge : 361.0370 centred at (gu) : 92.66820 90.42432 91.30562 assigned negative charge : -357.5376 centred at (gu) : 93.41945 90.77794 91.65944 start vw surface at 0.1400000 fill in re-entrant regions at 0.8400000 boundary points on vw surface= 195729 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20924 grid for indexing accessible points = 1.400000 m= 102757 mr = 142851 m= 39309 mr = 84698 m= 10538 mr = 31778 m= 1970 mr = 8019 m= 178 mr = 1411 m= 7 mr = 97 m= 0 mr = 2 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 1039 time to turn everything in is 1.850000 number of dielectric boundary points 81632 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.980000 number of grid points assigned charge 17872 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) : 2.100873 object centre at (A) : 6.159501 4.867000 26.27200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5296782 -1.7849833E-02 midg,1,midg; midg,igrid,midg -0.3278870 -0.6385880 1,midg,midg; igrid,midg,midg -7.2501414E-02 -0.6463202 gauss-seidel spectral radius is 0.9993074 estimated iterations to convergence 300 setup time was (sec) 2.140000 now iterating at: 13:52:02 rms-change max change #iterations 11.09651 409.8919 at 10iterations 6.629732 136.8828 at 20iterations 3.940593 78.70437 at 30iterations 2.339016 40.05063 at 40iterations 1.385059 25.67522 at 50iterations 0.8173831 14.61003 at 60iterations 0.4830239 8.600862 at 70iterations 0.2841098 5.014206 at 80iterations 0.1674083 2.719833 at 90iterations 9.8773032E-02 1.555518 at 100iterations 5.8173988E-02 0.9381521 at 110iterations 3.4578901E-02 0.5849018 at 120iterations 2.0605538E-02 0.3613815 at 130iterations 1.2476856E-02 0.2158127 at 140iterations 7.7793468E-03 0.1491089 at 150iterations 5.0673806E-03 9.9845886E-02 at 160iterations 3.4977712E-03 7.1376801E-02 at 170iterations 2.5714338E-03 5.1601410E-02 at 180iterations finished qdiffx linear iterations at : 13:52:11 total time elapsed so far: 11.90000 # loops : 180 mean,max change (kT/e) : 2.5714338E-03 5.1601410E-02 energy calculations done at 11.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.07000 DelPhi exited at 13:52:12 12.072u 0.158s 0:12.51 97.6% 0+0k 0+0io 0pf+0w