Sat Oct 15 15:15:07 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 Sat Oct 15 2011 at 15:15:07 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2789 !!! WARNING: HIR 72 has a net charge of 0.5140 !!! WARNING: SEP 229 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6637704 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): -4.196000 42.05600 ymin,ymax (A): -2.814000 48.85800 zmin,zma (A): 40.99000 94.62300 x,y,z range (A): 46.25200 51.67200 53.63300 scale (grids/A): 0.6637704 object centre (A): 18.93000 23.02200 67.80650 number of atom coordinates read : 2789 total number of charged atoms : 2640 net assigned charge : 5.039016 assigned positive charge : 427.0858 centred at (gu) : 89.96670 91.54325 90.39480 assigned negative charge : -422.0473 centred at (gu) : 89.70113 91.38950 90.51081 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8221 nv = 96 ne = 84 npr = 57137 no. pairs analyzed = 57137 no. exposed pairs = 3368 no. arc points = 23491 no. surface atoms = 1137 nbur = 1652 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 502 mr = 4667 m= 4 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.3100000 number of dielectric boundary points 3998 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2339 ## 218 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9723 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.7686512E-08 -1.5254232E-08 midg,1,midg; midg,igrid,midg -1.6557115E-08 6.8512790E-08 1,midg,midg; igrid,midg,midg -5.1135832E-08 7.4328909E-08 gauss-seidel spectral radius is 0.9882497 estimated iterations to convergence 75 setup time was (sec) 0.5900000 now iterating at: 15:15:08 rms-change max change #iterations 0.1828640 27.52707 at 10iterations 2.0276427E-02 2.500718 at 20iterations 2.2393486E-03 0.2754354 at 30iterations 3.2668008E-04 4.3754578E-02 at 40iterations 8.6209482E-05 1.1890411E-02 at 50iterations finished qdiffx linear iterations at : 15:15:11 total time elapsed so far: 4.050000 # loops : 50 mean,max change (kT/e) : 8.6209482E-05 1.1890411E-02 energy calculations done at 4.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.230000 DelPhi exited at 15:15:12 4.237u 0.234s 0:04.80 92.9% 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 Sat Oct 15 2011 at 15:15:12 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2789 !!! WARNING: HIR 72 has a net charge of 0.5140 !!! WARNING: SEP 229 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.991311 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): -4.196000 42.05600 ymin,ymax (A): -2.814000 48.85800 zmin,zma (A): 40.99000 94.62300 x,y,z range (A): 46.25200 51.67200 53.63300 scale (grids/A): 1.991311 object centre (A): 18.93000 23.02200 67.80650 number of atom coordinates read : 2789 total number of charged atoms : 2640 net assigned charge : 5.039016 assigned positive charge : 427.0858 centred at (gu) : 89.89948 94.62953 91.18398 assigned negative charge : -422.0473 centred at (gu) : 89.10302 94.16834 91.53236 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 87583 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23491 grid for indexing accessible points = 1.400000 m= 32848 mr = 61752 m= 5783 mr = 24541 m= 439 mr = 3645 m= 4 mr = 171 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 328 time to turn everything in is 0.6600000 number of dielectric boundary points 36548 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 160 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 20868 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) : 0.6637704 object centre at (A) : 18.93000 23.02200 67.80650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8074123E-02 -2.3102880E-02 midg,1,midg; midg,igrid,midg -4.2246780E-03 2.8462153E-02 1,midg,midg; igrid,midg,midg -3.0212846E-02 8.2852818E-02 gauss-seidel spectral radius is 0.9987632 estimated iterations to convergence 225 setup time was (sec) 1.000000 now iterating at: 15:15:13 rms-change max change #iterations 4.881461 200.9542 at 10iterations 2.363069 76.44483 at 20iterations 1.152717 34.69065 at 30iterations 0.5593224 16.88274 at 40iterations 0.2718226 7.593245 at 50iterations 0.1319294 3.868078 at 60iterations 6.4208813E-02 1.991177 at 70iterations 3.1275328E-02 0.9605789 at 80iterations 1.5319005E-02 0.4525795 at 90iterations 7.4739591E-03 0.2042694 at 100iterations 3.6733884E-03 0.1057167 at 110iterations 1.8274910E-03 5.5015564E-02 at 120iterations finished qdiffx linear iterations at : 15:15:22 total time elapsed so far: 9.800000 # loops : 120 mean,max change (kT/e) : 1.8274910E-03 5.5015564E-02 energy calculations done at 9.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.980000 DelPhi exited at 15:15:22 9.981u 0.284s 0:10.57 97.0% 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 Sat Oct 15 2011 at 15:15:22 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2789 !!! WARNING: HIR 72 has a net charge of 0.5140 !!! WARNING: SEP 229 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.986967 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): -4.196000 42.05600 ymin,ymax (A): -2.814000 48.85800 zmin,zma (A): 40.99000 94.62300 x,y,z range (A): 46.25200 51.67200 53.63300 scale (grids/A): 2.986967 object centre (A): 18.93000 23.02200 67.80650 number of atom coordinates read : 2789 total number of charged atoms : 2640 net assigned charge : 5.039016 assigned positive charge : 427.0858 centred at (gu) : 89.84930 96.94421 91.77568 assigned negative charge : -422.0473 centred at (gu) : 88.65446 96.25246 92.29839 start vw surface at 0.1400000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 202496 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23491 grid for indexing accessible points = 1.400000 m= 105116 mr = 149315 m= 39922 mr = 86748 m= 10569 mr = 32360 m= 1836 mr = 7949 m= 134 mr = 1243 m= 1 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 1271 time to turn everything in is 1.740000 number of dielectric boundary points 82403 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.890000 number of grid points assigned charge 21120 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) : 1.991311 object centre at (A) : 18.93000 23.02200 67.80650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2185977 -0.2902521 midg,1,midg; midg,igrid,midg 1.3268539E-02 8.0835797E-02 1,midg,midg; igrid,midg,midg -0.3127370 0.8296884 gauss-seidel spectral radius is 0.9992890 estimated iterations to convergence 296 setup time was (sec) 2.100000 now iterating at: 15:15:25 rms-change max change #iterations 11.11866 446.2031 at 10iterations 6.529615 139.0331 at 20iterations 3.837190 70.99994 at 30iterations 2.250797 41.72048 at 40iterations 1.315720 21.77473 at 50iterations 0.7694767 12.87447 at 60iterations 0.4492820 7.413714 at 70iterations 0.2622105 4.858409 at 80iterations 0.1530450 2.525373 at 90iterations 8.9338616E-02 1.765058 at 100iterations 5.1972471E-02 0.9723016 at 110iterations 3.0294728E-02 0.4933908 at 120iterations 1.7677110E-02 0.2918406 at 130iterations 1.0364280E-02 0.1813097 at 140iterations 6.1265528E-03 0.1029282 at 150iterations 3.6624598E-03 7.1445465E-02 at 160iterations 2.2405384E-03 4.6478271E-02 at 170iterations 1.4216534E-03 3.0029297E-02 at 180iterations finished qdiffx linear iterations at : 15:15:39 total time elapsed so far: 16.25000 # loops : 180 mean,max change (kT/e) : 1.4216534E-03 3.0029297E-02 energy calculations done at 16.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.43000 DelPhi exited at 15:15:39 16.432u 0.294s 0:17.19 97.2% 0+0k 0+0io 0pf+0w