Mon Oct 10 14:00:27 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 Mon Oct 10 2011 at 14:00:27 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4597 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5468006 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): 16.76600 78.49100 ymin,ymax (A): 119.0340 184.1400 zmin,zma (A): -1.855000 59.45200 x,y,z range (A): 61.72500 65.10600 61.30700 scale (grids/A): 0.5468006 object centre (A): 47.62850 151.5870 28.79850 number of atom coordinates read : 4597 total number of charged atoms : 4413 net assigned charge : 3.000041 assigned positive charge : 703.4697 centred at (gu) : 91.71919 89.24457 87.27892 assigned negative charge : -700.4730 centred at (gu) : 91.67848 89.16055 87.29459 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8770 nv = 96 ne = 84 npr = 92962 no. pairs analyzed = 92962 no. exposed pairs = 5504 no. arc points = 38416 no. surface atoms = 1855 nbur = 2742 mkacc time = 0.2300000 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 = 1.568000 m= 399 mr = 4749 m= 0 mr = 18 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 4402 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3960 ## 520 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 11741 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.9153472E-10 1.2051078E-11 midg,1,midg; midg,igrid,midg -8.7248697E-10 8.8687357E-10 1,midg,midg; igrid,midg,midg -1.6106894E-10 9.4700525E-10 gauss-seidel spectral radius is 0.9828741 estimated iterations to convergence 63 setup time was (sec) 0.7600000 now iterating at: 14:00:28 rms-change max change #iterations 9.3637504E-02 16.54261 at 10iterations 6.7458726E-03 1.024712 at 20iterations 8.1471505E-04 0.1200352 at 30iterations 2.0995390E-04 2.8330803E-02 at 40iterations 6.4237662E-05 9.3040466E-03 at 50iterations finished qdiffx linear iterations at : 14:00:32 total time elapsed so far: 4.130000 # loops : 50 mean,max change (kT/e) : 6.4237662E-05 9.3040466E-03 energy calculations done at 4.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.320000 DelPhi exited at 14:00:33 4.323u 0.216s 0:05.16 87.7% 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 Mon Oct 10 2011 at 14:00:33 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4597 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.640402 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): 16.76600 78.49100 ymin,ymax (A): 119.0340 184.1400 zmin,zma (A): -1.855000 59.45200 x,y,z range (A): 61.72500 65.10600 61.30700 scale (grids/A): 1.640402 object centre (A): 47.62850 151.5870 28.79850 number of atom coordinates read : 4597 total number of charged atoms : 4413 net assigned charge : 3.000041 assigned positive charge : 703.4697 centred at (gu) : 95.15594 87.73223 81.83578 assigned negative charge : -700.4730 centred at (gu) : 95.03531 87.48142 81.88343 start vw surface at 0.2100000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 98794 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38416 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 30974 mr = 69392 m= 3540 mr = 21542 m= 120 mr = 1940 m= 0 mr = 23 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 523 time to turn everything in is 0.7900000 number of dielectric boundary points 40531 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 447 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 33839 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) : 0.5468006 object centre at (A) : 47.62850 151.5870 28.79850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8331056E-03 9.3288012E-03 midg,1,midg; midg,igrid,midg 1.5371488E-02 3.1808197E-02 1,midg,midg; igrid,midg,midg -1.1654177E-02 -1.4028531E-02 gauss-seidel spectral radius is 0.9983535 estimated iterations to convergence 196 setup time was (sec) 1.120000 now iterating at: 14:00:34 rms-change max change #iterations 4.362615 191.7742 at 10iterations 1.890264 70.37454 at 20iterations 0.8199066 29.95872 at 30iterations 0.3566443 11.46319 at 40iterations 0.1557146 4.772464 at 50iterations 6.7706063E-02 2.131098 at 60iterations 2.9612361E-02 0.8480148 at 70iterations 1.2886041E-02 0.3737850 at 80iterations 5.6508309E-03 0.1699791 at 90iterations 2.4934728E-03 7.4132919E-02 at 100iterations 1.1167137E-03 3.1516254E-02 at 110iterations 5.1048823E-04 1.5830994E-02 at 120iterations finished qdiffx linear iterations at : 14:00:43 total time elapsed so far: 9.640000 # loops : 120 mean,max change (kT/e) : 5.1048823E-04 1.5830994E-02 energy calculations done at 9.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.830000 DelPhi exited at 14:00:44 9.831u 0.272s 0:11.55 87.4% 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 Mon Oct 10 2011 at 14:00:45 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: 342 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4597 !!! WARNING: FAD 994 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.460603 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): 16.76600 78.49100 ymin,ymax (A): 119.0340 184.1400 zmin,zma (A): -1.855000 59.45200 x,y,z range (A): 61.72500 65.10600 61.30700 scale (grids/A): 2.460603 object centre (A): 47.62850 151.5870 28.79850 number of atom coordinates read : 4597 total number of charged atoms : 4413 net assigned charge : 3.000041 assigned positive charge : 703.4697 centred at (gu) : 97.73355 86.59819 77.75340 assigned negative charge : -700.4730 centred at (gu) : 97.55292 86.22217 77.82510 start vw surface at 0.2400000 fill in re-entrant regions at 0.7000000 boundary points on vw surface= 230065 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38416 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 107150 mr = 169610 m= 31236 mr = 85506 m= 5836 mr = 23708 m= 501 mr = 4145 m= 21 mr = 296 m= 0 mr = 3 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 1656 time to turn everything in is 1.900000 number of dielectric boundary points 91541 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 2.050000 number of grid points assigned charge 35273 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) : 1.640402 object centre at (A) : 47.62850 151.5870 28.79850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1866067E-02 0.1935267 midg,1,midg; midg,igrid,midg 0.2368651 0.5679160 1,midg,midg; igrid,midg,midg -0.1622613 -0.2590474 gauss-seidel spectral radius is 0.9992189 estimated iterations to convergence 282 setup time was (sec) 2.240000 now iterating at: 14:00:47 rms-change max change #iterations 11.18923 462.8383 at 10iterations 6.467294 168.8245 at 20iterations 3.717409 73.89184 at 30iterations 2.131005 40.94160 at 40iterations 1.217708 22.66064 at 50iterations 0.6955779 12.65527 at 60iterations 0.3954137 6.792656 at 70iterations 0.2244395 3.913124 at 80iterations 0.1275392 2.299389 at 90iterations 7.2413139E-02 1.264827 at 100iterations 4.0932093E-02 0.7616577 at 110iterations 2.3240564E-02 0.4132156 at 120iterations 1.3178085E-02 0.2201004 at 130iterations 7.4656126E-03 0.1240597 at 140iterations 4.2296886E-03 6.9688797E-02 at 150iterations 2.3950476E-03 4.1179180E-02 at 160iterations 1.3549768E-03 2.2638321E-02 at 170iterations 7.6993776E-04 1.4942169E-02 at 180iterations finished qdiffx linear iterations at : 14:01:01 total time elapsed so far: 15.68000 # loops : 180 mean,max change (kT/e) : 7.6993776E-04 1.4942169E-02 energy calculations done at 15.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.87000 DelPhi exited at 14:01:02 15.872u 0.287s 0:17.71 91.1% 0+0k 0+0io 0pf+0w