Sun Oct 9 21:09:20 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 21:09:20 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2574 !!! WARNING: SEP 142 has a net charge of -0.4750 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: 0.6198419 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): -17.87200 39.56200 ymin,ymax (A): -53.91000 -7.188000 zmin,zma (A): -14.52500 40.33500 x,y,z range (A): 57.43400 46.72200 54.86000 scale (grids/A): 0.6198419 object centre (A): 10.84500 -30.54900 12.90500 number of atom coordinates read : 2574 total number of charged atoms : 2428 net assigned charge : 3.525005 assigned positive charge : 388.9009 centred at (gu) : 88.88234 89.51048 90.06311 assigned negative charge : -385.3766 centred at (gu) : 88.80148 89.46675 90.07124 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6480 nv = 96 ne = 84 npr = 52763 no. pairs analyzed = 52763 no. exposed pairs = 3072 no. arc points = 22420 no. surface atoms = 1034 nbur = 1540 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 327 mr = 3463 m= 0 mr = 47 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.3000000 number of dielectric boundary points 3297 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2253 ## 267 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8050 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.3924246E-09 2.4042266E-09 midg,1,midg; midg,igrid,midg 7.5186246E-12 5.1774567E-09 1,midg,midg; igrid,midg,midg -3.2010867E-09 6.3912116E-09 gauss-seidel spectral radius is 0.9865193 estimated iterations to convergence 71 setup time was (sec) 0.6100000 now iterating at: 21:09:21 rms-change max change #iterations 0.1275766 22.06224 at 10iterations 1.1668223E-02 1.830719 at 20iterations 1.0714075E-03 0.1584339 at 30iterations 9.9065102E-05 1.5556335E-02 at 40iterations 9.1576348E-06 1.3885498E-03 at 50iterations finished qdiffx linear iterations at : 21:09:24 total time elapsed so far: 4.370000 # loops : 50 mean,max change (kT/e) : 9.1576348E-06 1.3885498E-03 energy calculations done at 4.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.520000 DelPhi exited at 21:09:25 4.529u 0.402s 0:05.18 94.9% 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 Sun Oct 9 2011 at 21:09:25 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2574 !!! WARNING: SEP 142 has a net charge of -0.4750 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: 1.859526 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): -17.87200 39.56200 ymin,ymax (A): -53.91000 -7.188000 zmin,zma (A): -14.52500 40.33500 x,y,z range (A): 57.43400 46.72200 54.86000 scale (grids/A): 1.859526 object centre (A): 10.84500 -30.54900 12.90500 number of atom coordinates read : 2574 total number of charged atoms : 2428 net assigned charge : 3.525005 assigned positive charge : 388.9009 centred at (gu) : 86.64661 88.53108 90.18879 assigned negative charge : -385.3766 centred at (gu) : 86.40423 88.39984 90.21331 start vw surface at 0.1200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 69784 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22420 grid for indexing accessible points = 1.400000 m= 23318 mr = 47377 m= 3436 mr = 16630 m= 176 mr = 2138 m= 0 mr = 66 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 1365 time to turn everything in is 0.5600000 number of dielectric boundary points 30503 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 195 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 19059 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) : 0.6198419 object centre at (A) : 10.84500 -30.54900 12.90500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1175547E-02 2.7898194E-02 midg,1,midg; midg,igrid,midg -1.8002495E-02 -8.8365545E-04 1,midg,midg; igrid,midg,midg -3.9305277E-03 5.5865936E-02 gauss-seidel spectral radius is 0.9985613 estimated iterations to convergence 209 setup time was (sec) 0.9000000 now iterating at: 21:09:26 rms-change max change #iterations 4.005157 163.7672 at 10iterations 1.829049 61.79228 at 20iterations 0.8392029 29.40059 at 30iterations 0.3832911 12.66840 at 40iterations 0.1759675 6.162235 at 50iterations 8.0789573E-02 3.056915 at 60iterations 3.7030511E-02 1.220754 at 70iterations 1.6947284E-02 0.5608311 at 80iterations 7.7608372E-03 0.2627444 at 90iterations 3.5526336E-03 0.1131349 at 100iterations 1.6383327E-03 5.3214721E-02 at 110iterations 7.5178081E-04 2.3891926E-02 at 120iterations finished qdiffx linear iterations at : 21:09:36 total time elapsed so far: 10.51000 # loops : 120 mean,max change (kT/e) : 7.5178081E-04 2.3891926E-02 energy calculations done at 10.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.69000 DelPhi exited at 21:09:36 10.690u 0.439s 0:11.42 97.3% 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 21:09:36 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2574 !!! WARNING: SEP 142 has a net charge of -0.4750 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: 2.789289 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): -17.87200 39.56200 ymin,ymax (A): -53.91000 -7.188000 zmin,zma (A): -14.52500 40.33500 x,y,z range (A): 57.43400 46.72200 54.86000 scale (grids/A): 2.789289 object centre (A): 10.84500 -30.54900 12.90500 number of atom coordinates read : 2574 total number of charged atoms : 2428 net assigned charge : 3.525005 assigned positive charge : 388.9009 centred at (gu) : 84.96976 87.79639 90.28307 assigned negative charge : -385.3766 centred at (gu) : 84.60622 87.59981 90.31992 start vw surface at 0.1300000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 161509 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22420 grid for indexing accessible points = 1.400000 m= 76874 mr = 115224 m= 25971 mr = 61967 m= 6150 mr = 20309 m= 900 mr = 4638 m= 50 mr = 604 m= 0 mr = 15 time to grow re-entrant surface = 0.8500000 no. cavity mid-points inaccessible to solvent = 4402 time to turn everything in is 1.460000 number of dielectric boundary points 68697 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 19422 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) : 1.859526 object centre at (A) : 10.84500 -30.54900 12.90500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1525970 0.3169323 midg,1,midg; midg,igrid,midg -0.1485004 -3.7386645E-02 1,midg,midg; igrid,midg,midg -0.1487585 0.7200665 gauss-seidel spectral radius is 0.9992377 estimated iterations to convergence 286 setup time was (sec) 1.780000 now iterating at: 21:09:38 rms-change max change #iterations 9.467371 313.2224 at 10iterations 5.455272 135.0136 at 20iterations 3.117779 66.21449 at 30iterations 1.779715 35.67912 at 40iterations 1.013518 18.51778 at 50iterations 0.5779693 11.18977 at 60iterations 0.3291958 6.039009 at 70iterations 0.1871835 3.765564 at 80iterations 0.1063521 2.046659 at 90iterations 6.0624130E-02 1.133534 at 100iterations 3.4519192E-02 0.6345406 at 110iterations 1.9600879E-02 0.3587551 at 120iterations 1.1147381E-02 0.2072682 at 130iterations 6.3434881E-03 0.1198826 at 140iterations 3.6082591E-03 6.3616514E-02 at 150iterations 2.0541563E-03 3.6075592E-02 at 160iterations 1.1674406E-03 2.1289825E-02 at 170iterations 6.6290423E-04 1.1778355E-02 at 180iterations finished qdiffx linear iterations at : 21:09:55 total time elapsed so far: 17.81000 # loops : 180 mean,max change (kT/e) : 6.6290423E-04 1.1778355E-02 energy calculations done at 17.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.99000 DelPhi exited at 21:09:55 17.991u 0.456s 0:18.76 98.2% 0+0k 0+0io 0pf+0w