Tue Oct 11 06:23:10 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 06:23:10 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 = 2045 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: 0.7175683 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): 3.378000 47.25000 ymin,ymax (A): 0.6230000 42.32800 zmin,zma (A): -2.586000 47.02600 x,y,z range (A): 43.87200 41.70500 49.61200 scale (grids/A): 0.7175683 object centre (A): 25.31400 21.47550 22.22000 number of atom coordinates read : 2045 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 89.86559 89.94720 90.28751 assigned negative charge : -304.2972 centred at (gu) : 90.04850 89.92521 90.32167 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7190 nv = 96 ne = 84 npr = 41112 no. pairs analyzed = 41112 no. exposed pairs = 2458 no. arc points = 16743 no. surface atoms = 842 nbur = 1203 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 468 mr = 4196 m= 9 mr = 78 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3393 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1599 ## 176 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7912 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.5420653E-08 6.2698064E-08 midg,1,midg; midg,igrid,midg 6.7541315E-08 9.2486502E-08 1,midg,midg; igrid,midg,midg 1.9342582E-07 -3.1149483E-08 gauss-seidel spectral radius is 0.9898704 estimated iterations to convergence 81 setup time was (sec) 0.3600000 now iterating at: 06:23:11 rms-change max change #iterations 0.2166599 30.22806 at 10iterations 2.7489401E-02 3.807689 at 20iterations 3.6710741E-03 0.5586777 at 30iterations 5.8767362E-04 7.4920654E-02 at 40iterations 1.2999037E-04 1.6651154E-02 at 50iterations finished qdiffx linear iterations at : 06:23:13 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 1.2999037E-04 1.6651154E-02 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 06:23:14 3.399u 0.180s 0:03.99 89.4% 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 06:23:14 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 = 2045 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: 2.152705 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): 3.378000 47.25000 ymin,ymax (A): 0.6230000 42.32800 zmin,zma (A): -2.586000 47.02600 x,y,z range (A): 43.87200 41.70500 49.61200 scale (grids/A): 2.152705 object centre (A): 25.31400 21.47550 22.22000 number of atom coordinates read : 2045 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 89.59682 89.84162 90.86240 assigned negative charge : -304.2972 centred at (gu) : 90.14550 89.77570 90.96510 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 76244 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16743 grid for indexing accessible points = 1.400000 m= 30823 mr = 54572 m= 6192 mr = 23622 m= 554 mr = 4074 m= 13 mr = 259 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 31299 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 68 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 15334 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) : 0.7175683 object centre at (A) : 25.31400 21.47550 22.22000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0443606E-02 7.0431024E-02 midg,1,midg; midg,igrid,midg 6.9726114E-03 2.7796647E-02 1,midg,midg; igrid,midg,midg 4.9565259E-02 9.1422675E-03 gauss-seidel spectral radius is 0.9988553 estimated iterations to convergence 234 setup time was (sec) 0.6100000 now iterating at: 06:23:15 rms-change max change #iterations 4.639086 206.7940 at 10iterations 2.309999 73.78373 at 20iterations 1.159836 36.89019 at 30iterations 0.5767748 18.80923 at 40iterations 0.2903368 8.859844 at 50iterations 0.1448118 4.379077 at 60iterations 7.2665706E-02 2.400943 at 70iterations 3.6257394E-02 1.251511 at 80iterations 1.8176444E-02 0.5328827 at 90iterations 9.1526704E-03 0.2611222 at 100iterations 4.6407785E-03 0.1512330 at 110iterations 2.3687552E-03 7.0526123E-02 at 120iterations finished qdiffx linear iterations at : 06:23:22 total time elapsed so far: 7.790000 # loops : 120 mean,max change (kT/e) : 2.3687552E-03 7.0526123E-02 energy calculations done at 7.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.930000 DelPhi exited at 06:23:23 7.930u 0.187s 0:08.49 95.5% 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 Tue Oct 11 2011 at 06:23:23 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 = 2045 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: 3.229058 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): 3.378000 47.25000 ymin,ymax (A): 0.6230000 42.32800 zmin,zma (A): -2.586000 47.02600 x,y,z range (A): 43.87200 41.70500 49.61200 scale (grids/A): 3.229058 object centre (A): 25.31400 21.47550 22.22000 number of atom coordinates read : 2045 total number of charged atoms : 1929 net assigned charge : 7.500009 assigned positive charge : 311.7970 centred at (gu) : 89.39517 89.76247 91.29366 assigned negative charge : -304.2972 centred at (gu) : 90.21830 89.66356 91.44769 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 175626 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16743 grid for indexing accessible points = 1.400000 m= 96220 mr = 131157 m= 39542 mr = 80504 m= 11700 mr = 32626 m= 2325 mr = 9043 m= 260 mr = 1584 m= 6 mr = 170 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.190000 number of dielectric boundary points 70595 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 15432 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) : 2.152705 object centre at (A) : 25.31400 21.47550 22.22000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5128887 0.6352862 midg,1,midg; midg,igrid,midg 6.8884512E-04 0.2128082 1,midg,midg; igrid,midg,midg 0.3457319 0.1877521 gauss-seidel spectral radius is 0.9992982 estimated iterations to convergence 298 setup time was (sec) 1.430000 now iterating at: 06:23:24 rms-change max change #iterations 10.27951 314.0945 at 10iterations 6.101383 135.7935 at 20iterations 3.610706 73.18721 at 30iterations 2.127964 38.98409 at 40iterations 1.252996 23.94724 at 50iterations 0.7385086 13.81097 at 60iterations 0.4345523 7.382217 at 70iterations 0.2550393 4.466087 at 80iterations 0.1496469 3.161635 at 90iterations 8.7947600E-02 1.672904 at 100iterations 5.1764194E-02 0.8922434 at 110iterations 3.0512420E-02 0.5177631 at 120iterations 1.8161459E-02 0.3496208 at 130iterations 1.0940348E-02 0.1888618 at 140iterations 6.7641907E-03 0.1160660 at 150iterations 4.3351264E-03 8.8897705E-02 at 160iterations 2.9373050E-03 5.6003571E-02 at 170iterations 2.1185807E-03 3.9184570E-02 at 180iterations finished qdiffx linear iterations at : 06:23:36 total time elapsed so far: 12.73000 # loops : 180 mean,max change (kT/e) : 2.1185807E-03 3.9184570E-02 energy calculations done at 12.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.86000 DelPhi exited at 06:23:36 12.865u 0.234s 0:13.39 97.7% 0+0k 0+0io 0pf+0w