Mon Oct 10 13:54:48 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 Mon Oct 10 2011 at 13:54:48 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 = 2317 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: 0.6484163 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): -30.45200 24.45100 ymin,ymax (A): 27.55800 70.29300 zmin,zma (A): -13.39900 41.11400 x,y,z range (A): 54.90300 42.73500 54.51300 scale (grids/A): 0.6484163 object centre (A): -3.000500 48.92550 13.85750 number of atom coordinates read : 2317 total number of charged atoms : 2183 net assigned charge : 10.50002 assigned positive charge : 336.4426 centred at (gu) : 91.31247 91.37392 89.42734 assigned negative charge : -325.9433 centred at (gu) : 91.34760 91.26877 89.44736 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6840 nv = 96 ne = 84 npr = 45682 no. pairs analyzed = 45682 no. exposed pairs = 3104 no. arc points = 22211 no. surface atoms = 1048 nbur = 1269 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 445 mr = 3625 m= 7 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3610 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2170 ## 184 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7931 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4336607E-08 1.4907453E-08 midg,1,midg; midg,igrid,midg 4.8331326E-09 4.2599115E-08 1,midg,midg; igrid,midg,midg 1.7945895E-08 1.9381069E-08 gauss-seidel spectral radius is 0.9876620 estimated iterations to convergence 74 setup time was (sec) 0.3800000 now iterating at: 13:54:49 rms-change max change #iterations 0.1401072 20.55188 at 10iterations 1.4403445E-02 2.117714 at 20iterations 1.6048792E-03 0.2103596 at 30iterations 2.5550925E-04 4.2236328E-02 at 40iterations 6.0524741E-05 1.1230469E-02 at 50iterations finished qdiffx linear iterations at : 13:54:52 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 6.0524741E-05 1.1230469E-02 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 13:54:52 3.409u 0.176s 0:03.93 90.8% 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 13:54:52 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 = 2317 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: 1.945249 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): -30.45200 24.45100 ymin,ymax (A): 27.55800 70.29300 zmin,zma (A): -13.39900 41.11400 x,y,z range (A): 54.90300 42.73500 54.51300 scale (grids/A): 1.945249 object centre (A): -3.000500 48.92550 13.85750 number of atom coordinates read : 2317 total number of charged atoms : 2183 net assigned charge : 10.50002 assigned positive charge : 336.4426 centred at (gu) : 93.93724 94.12150 88.28186 assigned negative charge : -325.9433 centred at (gu) : 94.04292 93.80659 88.34214 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 72379 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22211 grid for indexing accessible points = 1.400000 m= 27461 mr = 48439 m= 5034 mr = 20087 m= 413 mr = 3241 m= 10 mr = 202 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 737 time to turn everything in is 0.3700000 number of dielectric boundary points 33328 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 148 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 17216 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) : 0.6484163 object centre at (A) : -3.000500 48.92550 13.85750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.3480422E-02 3.6751397E-02 midg,1,midg; midg,igrid,midg -1.6050939E-03 3.3444915E-02 1,midg,midg; igrid,midg,midg 5.6321718E-02 1.9197457E-02 gauss-seidel spectral radius is 0.9986731 estimated iterations to convergence 218 setup time was (sec) 0.6000000 now iterating at: 13:54:53 rms-change max change #iterations 3.995836 174.1444 at 10iterations 1.893026 64.31033 at 20iterations 0.8930004 36.43215 at 30iterations 0.4211966 13.85027 at 40iterations 0.1989325 7.200821 at 50iterations 9.3982585E-02 3.138860 at 60iterations 4.4471830E-02 1.391670 at 70iterations 2.1102635E-02 0.6457180 at 80iterations 9.9960901E-03 0.3228635 at 90iterations 4.7686710E-03 0.1535206 at 100iterations 2.2757940E-03 7.3592186E-02 at 110iterations 1.1008801E-03 3.7231445E-02 at 120iterations finished qdiffx linear iterations at : 13:55:00 total time elapsed so far: 7.760000 # loops : 120 mean,max change (kT/e) : 1.1008801E-03 3.7231445E-02 energy calculations done at 7.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 13:55:01 7.903u 0.195s 0:08.60 94.0% 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 Mon Oct 10 2011 at 13:55:02 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 = 2317 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: 2.917873 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): -30.45200 24.45100 ymin,ymax (A): 27.55800 70.29300 zmin,zma (A): -13.39900 41.11400 x,y,z range (A): 54.90300 42.73500 54.51300 scale (grids/A): 2.917873 object centre (A): -3.000500 48.92550 13.85750 number of atom coordinates read : 2317 total number of charged atoms : 2183 net assigned charge : 10.50002 assigned positive charge : 336.4426 centred at (gu) : 95.90578 96.18214 87.42273 assigned negative charge : -325.9433 centred at (gu) : 96.06436 95.70984 87.51328 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 166947 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22211 grid for indexing accessible points = 1.400000 m= 85293 mr = 117344 m= 33713 mr = 69123 m= 9224 mr = 27076 m= 1652 mr = 6992 m= 183 mr = 1202 m= 6 mr = 105 m= 0 mr = 0 time to grow re-entrant surface = 0.5500000 no. cavity mid-points inaccessible to solvent = 2570 time to turn everything in is 0.9600000 number of dielectric boundary points 75176 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 17464 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) : 1.945249 object centre at (A) : -3.000500 48.92550 13.85750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6423001 0.3642925 midg,1,midg; midg,igrid,midg -8.5891290E-03 0.3250236 1,midg,midg; igrid,midg,midg 0.7412087 0.2375101 gauss-seidel spectral radius is 0.9992765 estimated iterations to convergence 293 setup time was (sec) 1.190000 now iterating at: 13:55:03 rms-change max change #iterations 9.621498 330.3845 at 10iterations 5.704803 146.3589 at 20iterations 3.362877 71.67821 at 30iterations 1.971246 45.67915 at 40iterations 1.151011 27.72945 at 50iterations 0.6721376 13.91790 at 60iterations 0.3923999 7.894901 at 70iterations 0.2284260 4.667749 at 80iterations 0.1324525 2.352730 at 90iterations 7.6879345E-02 1.503096 at 100iterations 4.4532627E-02 0.8796082 at 110iterations 2.5941372E-02 0.4793091 at 120iterations 1.5001301E-02 0.2827473 at 130iterations 8.6956006E-03 0.1644316 at 140iterations 5.0309962E-03 9.5914841E-02 at 150iterations 2.9166804E-03 6.1842918E-02 at 160iterations 1.6915146E-03 3.1627655E-02 at 170iterations 9.8220340E-04 1.8280029E-02 at 180iterations finished qdiffx linear iterations at : 13:55:15 total time elapsed so far: 12.51000 # loops : 180 mean,max change (kT/e) : 9.8220340E-04 1.8280029E-02 energy calculations done at 12.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.64000 DelPhi exited at 13:55:15 12.645u 0.208s 0:13.51 95.0% 0+0k 0+0io 0pf+0w