Tue Oct 11 04:56:04 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 04:56:04 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3403 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: 0.5042350 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): -17.46800 37.02000 ymin,ymax (A): -46.98400 12.25900 zmin,zma (A): 12.07600 82.67800 x,y,z range (A): 54.48800 59.24300 70.60201 scale (grids/A): 0.5042350 object centre (A): 9.776000 -17.36250 47.37700 number of atom coordinates read : 3403 total number of charged atoms : 3258 net assigned charge : 8.500010 assigned positive charge : 519.5147 centred at (gu) : 90.49029 88.27822 89.22622 assigned negative charge : -511.0158 centred at (gu) : 90.53935 88.31047 89.50835 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5701 nv = 96 ne = 84 npr = 64818 no. pairs analyzed = 64818 no. exposed pairs = 4567 no. arc points = 33222 no. surface atoms = 1533 nbur = 1870 mkacc time = 0.1100000 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 = 1.680000 m= 190 mr = 2663 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3229 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3264 ## 517 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 7553 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.7654020E-10 -2.6285032E-10 midg,1,midg; midg,igrid,midg 2.0825988E-10 2.7187166E-11 1,midg,midg; igrid,midg,midg 1.3641073E-10 1.9347782E-11 gauss-seidel spectral radius is 0.9798069 estimated iterations to convergence 58 setup time was (sec) 0.4200000 now iterating at: 04:56:05 rms-change max change #iterations 5.1735844E-02 8.827393 at 10iterations 2.9052282E-03 0.4794426 at 20iterations 2.8945121E-04 6.7653656E-02 at 30iterations 6.0362338E-05 1.6559601E-02 at 40iterations 1.4234484E-05 4.0588379E-03 at 50iterations finished qdiffx linear iterations at : 04:56:08 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 1.4234484E-05 4.0588379E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 04:56:08 3.449u 0.165s 0:04.05 88.8% 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 04:56:08 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3403 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: 1.512705 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): -17.46800 37.02000 ymin,ymax (A): -46.98400 12.25900 zmin,zma (A): 12.07600 82.67800 x,y,z range (A): 54.48800 59.24300 70.60201 scale (grids/A): 1.512705 object centre (A): 9.776000 -17.36250 47.37700 number of atom coordinates read : 3403 total number of charged atoms : 3258 net assigned charge : 8.500010 assigned positive charge : 519.5147 centred at (gu) : 91.47012 84.83397 87.67792 assigned negative charge : -511.0158 centred at (gu) : 91.61737 84.93100 88.52470 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 64496 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33222 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 17161 mr = 41612 m= 1233 mr = 10717 m= 24 mr = 405 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 100 time to turn everything in is 0.3100000 number of dielectric boundary points 30180 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 447 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 24401 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) : 0.5042350 object centre at (A) : 9.776000 -17.36250 47.37700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6267013E-02 -1.6378172E-02 midg,1,midg; midg,igrid,midg 1.3345517E-02 -2.4816585E-03 1,midg,midg; igrid,midg,midg 4.5148684E-03 -3.4566002E-04 gauss-seidel spectral radius is 0.9979349 estimated iterations to convergence 175 setup time was (sec) 0.5200000 now iterating at: 04:56:09 rms-change max change #iterations 3.025192 130.2412 at 10iterations 1.191314 46.61454 at 20iterations 0.4647639 18.65003 at 30iterations 0.1831606 7.524811 at 40iterations 7.1861126E-02 2.732024 at 50iterations 2.8323889E-02 1.076130 at 60iterations 1.1095799E-02 0.4688425 at 70iterations 4.3981955E-03 0.1721525 at 80iterations 1.7471187E-03 7.1958542E-02 at 90iterations 7.0164166E-04 3.2512665E-02 at 100iterations 2.9151447E-04 1.3351440E-02 at 110iterations 1.2710040E-04 6.1111450E-03 at 120iterations finished qdiffx linear iterations at : 04:56:16 total time elapsed so far: 7.580000 # loops : 120 mean,max change (kT/e) : 1.2710040E-04 6.1111450E-03 energy calculations done at 7.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 04:56:17 7.720u 0.207s 0:08.47 93.5% 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 04:56:17 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: 220 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3403 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: 2.269057 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): -17.46800 37.02000 ymin,ymax (A): -46.98400 12.25900 zmin,zma (A): 12.07600 82.67800 x,y,z range (A): 54.48800 59.24300 70.60201 scale (grids/A): 2.269057 object centre (A): 9.776000 -17.36250 47.37700 number of atom coordinates read : 3403 total number of charged atoms : 3258 net assigned charge : 8.500010 assigned positive charge : 519.5147 centred at (gu) : 92.20509 82.25073 86.51651 assigned negative charge : -511.0158 centred at (gu) : 92.42612 82.39642 87.78688 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 150179 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33222 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 63075 mr = 102930 m= 13974 mr = 47699 m= 1593 mr = 9398 m= 62 mr = 798 m= 0 mr = 7 time to grow re-entrant surface = 0.4100000 no. cavity mid-points inaccessible to solvent = 300 time to turn everything in is 0.7400000 number of dielectric boundary points 68051 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 46 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 25975 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) : 1.512705 object centre at (A) : 9.776000 -17.36250 47.37700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2494552 -0.2286212 midg,1,midg; midg,igrid,midg 0.2443564 -9.1580130E-02 1,midg,midg; igrid,midg,midg 8.3360031E-02 -1.6999846E-02 gauss-seidel spectral radius is 0.9990755 estimated iterations to convergence 260 setup time was (sec) 0.9700000 now iterating at: 04:56:18 rms-change max change #iterations 8.257224 259.3530 at 10iterations 4.583683 124.2172 at 20iterations 2.517880 62.70805 at 30iterations 1.376211 32.67666 at 40iterations 0.7497302 16.89727 at 50iterations 0.4080752 9.796684 at 60iterations 0.2205844 4.953392 at 70iterations 0.1193299 2.694292 at 80iterations 6.4621501E-02 1.452357 at 90iterations 3.4882750E-02 0.7819514 at 100iterations 1.8819217E-02 0.4558244 at 110iterations 1.0146032E-02 0.2689066 at 120iterations 5.4702302E-03 0.1258144 at 130iterations 2.9526695E-03 6.2746048E-02 at 140iterations 1.5896859E-03 3.2768250E-02 at 150iterations 8.5721794E-04 2.0721436E-02 at 160iterations 4.6259075E-04 1.0833740E-02 at 170iterations 2.5053776E-04 5.7201385E-03 at 180iterations finished qdiffx linear iterations at : 04:56:29 total time elapsed so far: 12.22000 # loops : 180 mean,max change (kT/e) : 2.5053776E-04 5.7201385E-03 energy calculations done at 12.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.36000 DelPhi exited at 04:56:30 12.367u 0.215s 0:12.93 97.2% 0+0k 0+0io 0pf+0w