Mon Oct 10 09:52:50 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 09:52:51 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2819 !!! WARNING: HIT 235 has a net charge of 0.5140 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: 0.5606565 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): 106.8570 170.3540 ymin,ymax (A): -43.52700 11.30900 zmin,zma (A): 46.62000 99.94500 x,y,z range (A): 63.49699 54.83600 53.32500 scale (grids/A): 0.5606565 object centre (A): 138.6055 -16.10900 73.28250 number of atom coordinates read : 2819 total number of charged atoms : 2671 net assigned charge : 8.014013 assigned positive charge : 414.5109 centred at (gu) : 90.91245 88.65205 89.37605 assigned negative charge : -406.4974 centred at (gu) : 91.06214 88.70579 89.27222 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5910 nv = 96 ne = 84 npr = 54126 no. pairs analyzed = 54126 no. exposed pairs = 4434 no. arc points = 31457 no. surface atoms = 1451 nbur = 1368 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 285 mr = 2441 m= 3 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3749 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3118 ## 354 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7579 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3973729E-10 1.6766100E-09 midg,1,midg; midg,igrid,midg 1.9910016E-09 2.4646721E-10 1,midg,midg; igrid,midg,midg 1.9330140E-09 -8.7445412E-10 gauss-seidel spectral radius is 0.9835957 estimated iterations to convergence 64 setup time was (sec) 0.5300000 now iterating at: 09:52:51 rms-change max change #iterations 8.1868149E-02 14.08615 at 10iterations 5.6386660E-03 1.054443 at 20iterations 4.1421963E-04 6.9018364E-02 at 30iterations 3.3842240E-05 5.8212280E-03 at 40iterations 3.9803963E-06 5.2690506E-04 at 50iterations finished qdiffx linear iterations at : 09:52:54 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 3.9803963E-06 5.2690506E-04 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 09:52:55 3.372u 0.143s 0:03.92 89.5% 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 09:52:55 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2819 !!! WARNING: HIT 235 has a net charge of 0.5140 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: 1.681970 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): 106.8570 170.3540 ymin,ymax (A): -43.52700 11.30900 zmin,zma (A): 46.62000 99.94500 x,y,z range (A): 63.49699 54.83600 53.32500 scale (grids/A): 1.681970 object centre (A): 138.6055 -16.10900 73.28250 number of atom coordinates read : 2819 total number of charged atoms : 2671 net assigned charge : 8.014013 assigned positive charge : 414.5109 centred at (gu) : 92.73688 85.95560 88.12770 assigned negative charge : -406.4974 centred at (gu) : 93.18615 86.11688 87.81670 start vw surface at 0.1600000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 62649 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31457 grid for indexing accessible points = 1.400000 m= 19751 mr = 36858 m= 2521 mr = 12194 m= 108 mr = 1173 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 21 time to turn everything in is 0.4700000 number of dielectric boundary points 34800 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 300 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 20580 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) : 0.5606565 object centre at (A) : 138.6055 -16.10900 73.28250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1137730E-03 1.8211696E-02 midg,1,midg; midg,igrid,midg 1.4277085E-02 7.1431124E-03 1,midg,midg; igrid,midg,midg 2.2769369E-02 1.8696994E-02 gauss-seidel spectral radius is 0.9983021 estimated iterations to convergence 193 setup time was (sec) 0.7300000 now iterating at: 09:52:55 rms-change max change #iterations 3.375504 158.2413 at 10iterations 1.440418 55.91858 at 20iterations 0.6141909 22.86640 at 30iterations 0.2602189 10.05938 at 40iterations 0.1115649 4.278085 at 50iterations 4.7686458E-02 1.780853 at 60iterations 2.0389885E-02 0.7738419 at 70iterations 8.7321745E-03 0.3167648 at 80iterations 3.7349183E-03 0.1446075 at 90iterations 1.6009758E-03 5.7373047E-02 at 100iterations 6.8501831E-04 2.6237488E-02 at 110iterations 2.9397869E-04 1.0666370E-02 at 120iterations finished qdiffx linear iterations at : 09:53:01 total time elapsed so far: 6.600000 # loops : 120 mean,max change (kT/e) : 2.9397869E-04 1.0666370E-02 energy calculations done at 6.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.770000 DelPhi exited at 09:53:02 6.776u 0.152s 0:07.28 95.0% 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 09:53:02 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2819 !!! WARNING: HIT 235 has a net charge of 0.5140 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: 2.522954 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): 106.8570 170.3540 ymin,ymax (A): -43.52700 11.30900 zmin,zma (A): 46.62000 99.94500 x,y,z range (A): 63.49699 54.83600 53.32500 scale (grids/A): 2.522954 object centre (A): 138.6055 -16.10900 73.28250 number of atom coordinates read : 2819 total number of charged atoms : 2671 net assigned charge : 8.014013 assigned positive charge : 414.5109 centred at (gu) : 94.10522 83.93321 87.19156 assigned negative charge : -406.4974 centred at (gu) : 94.77913 84.17522 86.72496 start vw surface at 0.1300000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 144539 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31457 grid for indexing accessible points = 1.400000 m= 64243 mr = 91266 m= 20625 mr = 46708 m= 4075 mr = 14624 m= 373 mr = 2484 m= 10 mr = 119 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 52 time to turn everything in is 1.050000 number of dielectric boundary points 78664 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 21353 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) : 1.681970 object centre at (A) : 138.6055 -16.10900 73.28250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.5783476E-02 0.2706523 midg,1,midg; midg,igrid,midg 0.2351521 0.1434996 1,midg,midg; igrid,midg,midg 0.2666047 0.2157910 gauss-seidel spectral radius is 0.9991896 estimated iterations to convergence 277 setup time was (sec) 1.330000 now iterating at: 09:53:03 rms-change max change #iterations 8.814164 305.2194 at 10iterations 5.074227 134.0685 at 20iterations 2.906636 68.09439 at 30iterations 1.653641 39.80715 at 40iterations 0.9360576 21.49685 at 50iterations 0.5290919 13.74751 at 60iterations 0.2975276 6.620230 at 70iterations 0.1676589 4.184593 at 80iterations 9.3991324E-02 2.275620 at 90iterations 5.2854225E-02 1.181610 at 100iterations 2.9598480E-02 0.6461372 at 110iterations 1.6616477E-02 0.4101601 at 120iterations 9.2826188E-03 0.1935089 at 130iterations 5.2026003E-03 0.1039715 at 140iterations 2.9069460E-03 6.2857479E-02 at 150iterations 1.6258012E-03 3.7935257E-02 at 160iterations 9.0877811E-04 1.9302368E-02 at 170iterations 5.0828978E-04 1.0135651E-02 at 180iterations finished qdiffx linear iterations at : 09:53:13 total time elapsed so far: 10.64000 # loops : 180 mean,max change (kT/e) : 5.0828978E-04 1.0135651E-02 energy calculations done at 10.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.81000 DelPhi exited at 09:53:13 10.817u 0.175s 0:11.41 96.2% 0+0k 0+0io 0pf+0w