Tue Oct 11 07:40:58 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 Tue Oct 11 2011 at 07:40:58 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2671 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: 0.6962916 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): -13.39400 37.73400 ymin,ymax (A): -22.30000 25.17700 zmin,zma (A): -6.080000 40.35200 x,y,z range (A): 51.12800 47.47700 46.43200 scale (grids/A): 0.6962916 object centre (A): 12.17000 1.438500 17.13600 number of atom coordinates read : 2671 total number of charged atoms : 2315 net assigned charge : 6.500009 assigned positive charge : 369.2081 centred at (gu) : 91.28860 88.67293 89.49918 assigned negative charge : -362.7086 centred at (gu) : 91.32132 88.68062 89.61959 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7967 nv = 96 ne = 84 npr = 50619 no. pairs analyzed = 50619 no. exposed pairs = 2893 no. arc points = 19850 no. surface atoms = 991 nbur = 1680 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 520 mr = 4659 m= 2 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3732 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1882 ## 177 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 9064 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0448866E-07 -1.1089019E-08 midg,1,midg; midg,igrid,midg 5.8307034E-08 2.9826722E-08 1,midg,midg; igrid,midg,midg 4.3885855E-08 3.4419557E-08 gauss-seidel spectral radius is 0.9892843 estimated iterations to convergence 79 setup time was (sec) 0.6900000 now iterating at: 07:40:59 rms-change max change #iterations 0.2048262 32.55766 at 10iterations 2.4930604E-02 3.520915 at 20iterations 3.2426524E-03 0.4089093 at 30iterations 5.2822620E-04 6.6024780E-02 at 40iterations 1.2457138E-04 1.7047882E-02 at 50iterations finished qdiffx linear iterations at : 07:41:02 total time elapsed so far: 4.230000 # loops : 50 mean,max change (kT/e) : 1.2457138E-04 1.7047882E-02 energy calculations done at 4.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.450000 DelPhi exited at 07:41:03 4.457u 0.409s 0:05.45 88.9% 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 Tue Oct 11 2011 at 07:41:03 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2671 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: 2.088875 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): -13.39400 37.73400 ymin,ymax (A): -22.30000 25.17700 zmin,zma (A): -6.080000 40.35200 x,y,z range (A): 51.12800 47.47700 46.43200 scale (grids/A): 2.088875 object centre (A): 12.17000 1.438500 17.13600 number of atom coordinates read : 2671 total number of charged atoms : 2315 net assigned charge : 6.500009 assigned positive charge : 369.2081 centred at (gu) : 93.86534 86.01864 88.49720 assigned negative charge : -362.7086 centred at (gu) : 93.96386 86.04168 88.85857 start vw surface at 0.1600000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 84588 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19850 grid for indexing accessible points = 1.400000 m= 33629 mr = 60367 m= 6398 mr = 25874 m= 546 mr = 4318 m= 8 mr = 284 m= 0 mr = 2 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9000000 number of dielectric boundary points 34324 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 95 iepsmp to db, and charging done at 1.130000 number of grid points assigned charge 18350 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) : 0.6962916 object centre at (A) : 12.17000 1.438500 17.13600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7351925E-02 -7.2859707E-03 midg,1,midg; midg,igrid,midg 1.7674264E-02 2.2898624E-02 1,midg,midg; igrid,midg,midg 2.2004129E-02 5.2545786E-02 gauss-seidel spectral radius is 0.9988288 estimated iterations to convergence 231 setup time was (sec) 1.320000 now iterating at: 07:41:05 rms-change max change #iterations 4.900141 219.1740 at 10iterations 2.432338 82.83121 at 20iterations 1.205930 35.75992 at 30iterations 0.5991611 16.41477 at 40iterations 0.2983466 8.402761 at 50iterations 0.1480674 4.094290 at 60iterations 7.3746324E-02 2.447647 at 70iterations 3.6726862E-02 1.093820 at 80iterations 1.8291680E-02 0.6050186 at 90iterations 9.1380300E-03 0.2646561 at 100iterations 4.5904373E-03 0.1505041 at 110iterations 2.3389449E-03 7.2914124E-02 at 120iterations finished qdiffx linear iterations at : 07:41:14 total time elapsed so far: 10.41000 # loops : 120 mean,max change (kT/e) : 2.3389449E-03 7.2914124E-02 energy calculations done at 10.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.64000 DelPhi exited at 07:41:15 10.642u 0.482s 0:11.38 97.7% 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 Tue Oct 11 2011 at 07:41:15 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2671 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: 3.133312 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): -13.39400 37.73400 ymin,ymax (A): -22.30000 25.17700 zmin,zma (A): -6.080000 40.35200 x,y,z range (A): 51.12800 47.47700 46.43200 scale (grids/A): 3.133312 object centre (A): 12.17000 1.438500 17.13600 number of atom coordinates read : 2671 total number of charged atoms : 2315 net assigned charge : 6.500009 assigned positive charge : 369.2081 centred at (gu) : 95.79806 84.02777 87.74560 assigned negative charge : -362.7086 centred at (gu) : 95.94573 84.06252 88.28783 start vw surface at 0.1600000 fill in re-entrant regions at 1.120000 boundary points on vw surface= 194926 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19850 grid for indexing accessible points = 1.400000 m= 105328 mr = 145018 m= 42613 mr = 88443 m= 11981 mr = 35430 m= 2283 mr = 9299 m= 283 mr = 1653 m= 7 mr = 181 m= 0 mr = 2 time to grow re-entrant surface = 1.470000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.730000 number of dielectric boundary points 77395 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.890000 number of grid points assigned charge 18518 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) : 2.088875 object centre at (A) : 12.17000 1.438500 17.13600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8957994E-02 -0.1094298 midg,1,midg; midg,igrid,midg 0.1237115 0.1156762 1,midg,midg; igrid,midg,midg 6.9839694E-02 0.2813825 gauss-seidel spectral radius is 0.9992980 estimated iterations to convergence 298 setup time was (sec) 3.100000 now iterating at: 07:41:18 rms-change max change #iterations 10.81812 413.2463 at 10iterations 6.360564 147.3098 at 20iterations 3.741390 64.42586 at 30iterations 2.189917 37.28577 at 40iterations 1.284311 25.22271 at 50iterations 0.7506599 12.60615 at 60iterations 0.4389073 8.112259 at 70iterations 0.2570824 4.576344 at 80iterations 0.1496468 2.553581 at 90iterations 8.7653130E-02 1.452408 at 100iterations 5.1215421E-02 0.8330593 at 110iterations 2.9984305E-02 0.5036736 at 120iterations 1.7606795E-02 0.2866096 at 130iterations 1.0411995E-02 0.1779766 at 140iterations 6.1945179E-03 0.1067657 at 150iterations 3.7579290E-03 6.0190201E-02 at 160iterations 2.3515909E-03 4.4620514E-02 at 170iterations 1.5294624E-03 2.6420593E-02 at 180iterations finished qdiffx linear iterations at : 07:41:37 total time elapsed so far: 22.28000 # loops : 180 mean,max change (kT/e) : 1.5294624E-03 2.6420593E-02 energy calculations done at 22.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.49000 DelPhi exited at 07:41:38 22.496u 0.502s 0:23.30 98.6% 0+0k 0+0io 0pf+0w