Sun Oct 9 16:17:52 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 16:17:52 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 = 3062 !!! WARNING: MG3 345 has a net charge of 1.4000 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: 0.6344002 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): -15.53900 37.16000 ymin,ymax (A): 54.22400 107.3640 zmin,zma (A): -4.495000 51.62100 x,y,z range (A): 52.69900 53.14000 56.11600 scale (grids/A): 0.6344002 object centre (A): 10.81050 80.79400 23.56300 number of atom coordinates read : 3062 total number of charged atoms : 2918 net assigned charge : -3.099983 assigned positive charge : 452.8991 centred at (gu) : 90.22912 88.77833 91.39141 assigned negative charge : -456.0005 centred at (gu) : 90.25971 88.65716 91.44370 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8127 nv = 96 ne = 84 npr = 63287 no. pairs analyzed = 63287 no. exposed pairs = 3645 no. arc points = 25760 no. surface atoms = 1232 nbur = 1830 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 455 mr = 4467 m= 3 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.3600000 number of dielectric boundary points 4045 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2589 ## 238 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9992 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8521076E-09 -1.3081649E-08 midg,1,midg; midg,igrid,midg -2.3378757E-08 7.9852320E-09 1,midg,midg; igrid,midg,midg 4.2093346E-11 -7.4631643E-09 gauss-seidel spectral radius is 0.9871687 estimated iterations to convergence 72 setup time was (sec) 0.6000000 now iterating at: 16:17:53 rms-change max change #iterations 0.1552577 21.03088 at 10iterations 1.4990352E-02 2.008778 at 20iterations 1.4898716E-03 0.2437439 at 30iterations 1.6229320E-04 2.1102905E-02 at 40iterations 3.6189918E-05 6.8190098E-03 at 50iterations finished qdiffx linear iterations at : 16:17:56 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 3.6189918E-05 6.8190098E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 16:17:56 3.398u 0.147s 0:03.87 91.2% 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 16:17:56 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 = 3062 !!! WARNING: MG3 345 has a net charge of 1.4000 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: 1.903201 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): -15.53900 37.16000 ymin,ymax (A): 54.22400 107.3640 zmin,zma (A): -4.495000 51.62100 x,y,z range (A): 52.69900 53.14000 56.11600 scale (grids/A): 1.903201 object centre (A): 10.81050 80.79400 23.56300 number of atom coordinates read : 3062 total number of charged atoms : 2918 net assigned charge : -3.099983 assigned positive charge : 452.8991 centred at (gu) : 90.68690 86.33441 94.17320 assigned negative charge : -456.0005 centred at (gu) : 90.77895 85.97138 94.33070 start vw surface at 0.1700000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 88099 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25760 grid for indexing accessible points = 1.400000 m= 31617 mr = 61607 m= 5479 mr = 23035 m= 372 mr = 3552 m= 8 mr = 141 m= 0 mr = 2 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 208 time to turn everything in is 0.6600000 number of dielectric boundary points 37238 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 178 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 22958 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) : 0.6344002 object centre at (A) : 10.81050 80.79400 23.56300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6717534E-02 8.1525128E-03 midg,1,midg; midg,igrid,midg -2.9339934E-02 -9.5073497E-03 1,midg,midg; igrid,midg,midg -3.4516275E-02 -2.3301296E-02 gauss-seidel spectral radius is 0.9986749 estimated iterations to convergence 218 setup time was (sec) 0.9500000 now iterating at: 16:17:57 rms-change max change #iterations 4.678172 204.4053 at 10iterations 2.204782 63.89876 at 20iterations 1.044387 31.15147 at 30iterations 0.4940054 14.31994 at 40iterations 0.2335328 6.923141 at 50iterations 0.1109351 3.483921 at 60iterations 5.2543003E-02 1.516112 at 70iterations 2.4798907E-02 0.7273560 at 80iterations 1.1812639E-02 0.3762507 at 90iterations 5.6054676E-03 0.1600952 at 100iterations 2.6708369E-03 7.9240799E-02 at 110iterations 1.2779138E-03 4.4475555E-02 at 120iterations finished qdiffx linear iterations at : 16:18:04 total time elapsed so far: 7.890000 # loops : 120 mean,max change (kT/e) : 1.2779138E-03 4.4475555E-02 energy calculations done at 7.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.090000 DelPhi exited at 16:18:05 8.093u 0.177s 0:08.54 96.7% 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 16:18:05 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 = 3062 !!! WARNING: MG3 345 has a net charge of 1.4000 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: 2.854801 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): -15.53900 37.16000 ymin,ymax (A): 54.22400 107.3640 zmin,zma (A): -4.495000 51.62100 x,y,z range (A): 52.69900 53.14000 56.11600 scale (grids/A): 2.854801 object centre (A): 10.81050 80.79400 23.56300 number of atom coordinates read : 3062 total number of charged atoms : 2918 net assigned charge : -3.099983 assigned positive charge : 452.8991 centred at (gu) : 91.03011 84.50127 96.25957 assigned negative charge : -456.0005 centred at (gu) : 91.16838 83.95699 96.49606 start vw surface at 0.1900000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 204299 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25760 grid for indexing accessible points = 1.400000 m= 101312 mr = 149629 m= 38173 mr = 82476 m= 10106 mr = 30510 m= 1548 mr = 7701 m= 90 mr = 1027 m= 1 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 726 time to turn everything in is 1.660000 number of dielectric boundary points 84143 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.800000 number of grid points assigned charge 23344 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) : 1.903201 object centre at (A) : 10.81050 80.79400 23.56300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5545750 0.2213930 midg,1,midg; midg,igrid,midg -0.3084215 -0.2599591 1,midg,midg; igrid,midg,midg -0.4959942 -0.2789301 gauss-seidel spectral radius is 0.9992777 estimated iterations to convergence 294 setup time was (sec) 1.960000 now iterating at: 16:18:07 rms-change max change #iterations 10.85674 409.9338 at 10iterations 6.386811 121.6531 at 20iterations 3.733804 77.01813 at 30iterations 2.175622 40.60423 at 40iterations 1.268120 25.14624 at 50iterations 0.7369789 14.00803 at 60iterations 0.4284100 7.487135 at 70iterations 0.2488928 4.616593 at 80iterations 0.1445959 2.543686 at 90iterations 8.3798222E-02 1.725790 at 100iterations 4.8616346E-02 0.8246384 at 110iterations 2.8164128E-02 0.4729156 at 120iterations 1.6301868E-02 0.2726481 at 130iterations 9.4657773E-03 0.1685867 at 140iterations 5.4774387E-03 9.5678329E-02 at 150iterations 3.1744763E-03 5.5228233E-02 at 160iterations 1.8395188E-03 2.9363632E-02 at 170iterations 1.0695579E-03 1.8324852E-02 at 180iterations finished qdiffx linear iterations at : 16:18:17 total time elapsed so far: 12.30000 # loops : 180 mean,max change (kT/e) : 1.0695579E-03 1.8324852E-02 energy calculations done at 12.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.49000 DelPhi exited at 16:18:18 12.492u 0.189s 0:12.97 97.6% 0+0k 0+0io 0pf+0w