Mon Oct 10 10:24:12 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 10:24:12 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2708 !!! WARNING: HIT 236 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5676382 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): -22.15800 40.55800 ymin,ymax (A): -11.04200 43.64100 zmin,zma (A): -1.582000 51.71000 x,y,z range (A): 62.71600 54.68300 53.29200 scale (grids/A): 0.5676382 object centre (A): 9.200001 16.29950 25.06400 number of atom coordinates read : 2708 total number of charged atoms : 2562 net assigned charge : 10.01403 assigned positive charge : 399.8921 centred at (gu) : 92.04090 91.03330 86.70300 assigned negative charge : -389.8786 centred at (gu) : 92.10970 91.04504 86.54803 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5798 nv = 96 ne = 84 npr = 52900 no. pairs analyzed = 52900 no. exposed pairs = 3968 no. arc points = 28719 no. surface atoms = 1324 nbur = 1384 mkacc time = 8.9999996E-02 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 = 1.512000 m= 233 mr = 2554 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3468 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2837 ## 312 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7384 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2235212E-09 1.5593354E-09 midg,1,midg; midg,igrid,midg 1.2773184E-09 1.6915815E-09 1,midg,midg; igrid,midg,midg 1.4444429E-09 9.6126762E-10 gauss-seidel spectral radius is 0.9839777 estimated iterations to convergence 65 setup time was (sec) 0.3900000 now iterating at: 10:24:13 rms-change max change #iterations 8.5121386E-02 16.62990 at 10iterations 6.1320425E-03 1.097784 at 20iterations 4.7129369E-04 8.8087082E-02 at 30iterations 3.8479571E-05 7.2975159E-03 at 40iterations 4.2177298E-06 5.4931641E-04 at 50iterations finished qdiffx linear iterations at : 10:24:15 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 4.2177298E-06 5.4931641E-04 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 10:24:16 3.428u 0.165s 0:03.93 91.0% 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 10:24:16 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2708 !!! WARNING: HIT 236 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.702915 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): -22.15800 40.55800 ymin,ymax (A): -11.04200 43.64100 zmin,zma (A): -1.582000 51.71000 x,y,z range (A): 62.71600 54.68300 53.29200 scale (grids/A): 1.702915 object centre (A): 9.200001 16.29950 25.06400 number of atom coordinates read : 2708 total number of charged atoms : 2562 net assigned charge : 10.01403 assigned positive charge : 399.8921 centred at (gu) : 96.12240 93.09940 80.10867 assigned negative charge : -389.8786 centred at (gu) : 96.32896 93.13496 79.64386 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 62008 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28719 grid for indexing accessible points = 1.400000 m= 18814 mr = 37988 m= 2191 mr = 11988 m= 68 mr = 980 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 32124 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 274 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 19817 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) : 0.5676382 object centre at (A) : 9.200001 16.29950 25.06400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9964618E-03 8.3258422E-03 midg,1,midg; midg,igrid,midg 1.7523590E-02 1.9019660E-02 1,midg,midg; igrid,midg,midg -1.6192665E-02 1.7098855E-02 gauss-seidel spectral radius is 0.9983112 estimated iterations to convergence 193 setup time was (sec) 0.5400000 now iterating at: 10:24:17 rms-change max change #iterations 3.372738 175.2706 at 10iterations 1.437613 53.37019 at 20iterations 0.6158445 26.05749 at 30iterations 0.2631891 10.11247 at 40iterations 0.1128737 4.092832 at 50iterations 4.8232071E-02 1.762077 at 60iterations 2.0608017E-02 0.7979889 at 70iterations 8.8573415E-03 0.4149323 at 80iterations 3.7972254E-03 0.1565636 at 90iterations 1.6281473E-03 6.1174393E-02 at 100iterations 6.9963856E-04 2.9453278E-02 at 110iterations 3.0076908E-04 1.0940552E-02 at 120iterations finished qdiffx linear iterations at : 10:24:24 total time elapsed so far: 7.620000 # loops : 120 mean,max change (kT/e) : 3.0076908E-04 1.0940552E-02 energy calculations done at 7.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 10:24:24 7.750u 0.200s 0:08.34 95.3% 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 Mon Oct 10 2011 at 10:24:24 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: 275 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2708 !!! WARNING: HIT 236 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.554372 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): -22.15800 40.55800 ymin,ymax (A): -11.04200 43.64100 zmin,zma (A): -1.582000 51.71000 x,y,z range (A): 62.71600 54.68300 53.29200 scale (grids/A): 2.554372 object centre (A): 9.200001 16.29950 25.06400 number of atom coordinates read : 2708 total number of charged atoms : 2562 net assigned charge : 10.01403 assigned positive charge : 399.8921 centred at (gu) : 99.18338 94.64907 75.16302 assigned negative charge : -389.8786 centred at (gu) : 99.49339 94.70235 74.46575 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 143535 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28719 grid for indexing accessible points = 1.400000 m= 63149 mr = 94047 m= 19286 mr = 47196 m= 3403 mr = 13739 m= 259 mr = 2070 m= 6 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7700000 number of dielectric boundary points 72491 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 20486 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) : 1.702915 object centre at (A) : 9.200001 16.29950 25.06400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1012813 8.8100687E-02 midg,1,midg; midg,igrid,midg 0.3202079 0.2482542 1,midg,midg; igrid,midg,midg -0.6743252 0.2679473 gauss-seidel spectral radius is 0.9991748 estimated iterations to convergence 275 setup time was (sec) 1.010000 now iterating at: 10:24:26 rms-change max change #iterations 8.779959 336.8941 at 10iterations 5.066304 136.4557 at 20iterations 2.905752 78.14929 at 30iterations 1.647292 49.38409 at 40iterations 0.9308077 27.26054 at 50iterations 0.5230852 14.20254 at 60iterations 0.2934699 7.550175 at 70iterations 0.1647217 3.933401 at 80iterations 9.1908768E-02 1.926414 at 90iterations 5.1387377E-02 1.094648 at 100iterations 2.8676469E-02 0.6505914 at 110iterations 1.6015381E-02 0.3672400 at 120iterations 8.9366464E-03 0.2073107 at 130iterations 4.9783257E-03 0.1143319 at 140iterations 2.7680143E-03 6.0829163E-02 at 150iterations 1.5438802E-03 3.1855464E-02 at 160iterations 8.5716491E-04 1.8966436E-02 at 170iterations 4.7843848E-04 1.0063171E-02 at 180iterations finished qdiffx linear iterations at : 10:24:37 total time elapsed so far: 12.24000 # loops : 180 mean,max change (kT/e) : 4.7843848E-04 1.0063171E-02 energy calculations done at 12.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.38000 DelPhi exited at 10:24:37 12.378u 0.214s 0:12.86 97.8% 0+0k 0+0io 0pf+0w