Tue Oct 11 08:39:40 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 08:39:40 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3233 !!! WARNING: UMP 529 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5947806 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): 0.3460000 48.77400 ymin,ymax (A): -8.444000 49.29500 zmin,zma (A): 0.6079999 60.46200 x,y,z range (A): 48.42800 57.73900 59.85400 scale (grids/A): 0.5947806 object centre (A): 24.56000 20.42550 30.53500 number of atom coordinates read : 3233 total number of charged atoms : 3088 net assigned charge : -1.099990 assigned positive charge : 486.5088 centred at (gu) : 89.75323 89.40965 91.10996 assigned negative charge : -487.6100 centred at (gu) : 89.64701 89.35981 91.03243 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7624 nv = 96 ne = 84 npr = 66229 no. pairs analyzed = 66229 no. exposed pairs = 3763 no. arc points = 25721 no. surface atoms = 1281 nbur = 1952 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 356 mr = 4469 m= 0 mr = 37 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 20 time to turn everything in is 0.3600000 number of dielectric boundary points 3474 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2624 ## 277 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9545 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.6710743E-09 3.3580418E-09 midg,1,midg; midg,igrid,midg -2.7014748E-09 1.3241950E-09 1,midg,midg; igrid,midg,midg -4.8605915E-09 3.4693040E-09 gauss-seidel spectral radius is 0.9854206 estimated iterations to convergence 68 setup time was (sec) 0.6000000 now iterating at: 08:39:40 rms-change max change #iterations 0.1176022 15.05267 at 10iterations 1.0648208E-02 1.557861 at 20iterations 1.5451137E-03 0.2629690 at 30iterations 5.4510054E-04 0.1010323 at 40iterations 2.1609943E-04 4.0500641E-02 at 50iterations finished qdiffx linear iterations at : 08:39:43 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 2.1609943E-04 4.0500641E-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) 3.460000 DelPhi exited at 08:39:44 3.466u 0.150s 0:04.19 86.1% 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 08:39:44 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3233 !!! WARNING: UMP 529 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.784342 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): 0.3460000 48.77400 ymin,ymax (A): -8.444000 49.29500 zmin,zma (A): 0.6079999 60.46200 x,y,z range (A): 48.42800 57.73900 59.85400 scale (grids/A): 1.784342 object centre (A): 24.56000 20.42550 30.53500 number of atom coordinates read : 3233 total number of charged atoms : 3088 net assigned charge : -1.099990 assigned positive charge : 486.5088 centred at (gu) : 89.25911 88.22838 93.32905 assigned negative charge : -487.6100 centred at (gu) : 88.94065 88.07910 93.09698 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 83335 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25721 grid for indexing accessible points = 1.400000 m= 31605 mr = 60068 m= 4354 mr = 24375 m= 169 mr = 2763 m= 4 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 1243 time to turn everything in is 0.6100000 number of dielectric boundary points 32205 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 223 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 24078 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) : 0.5947806 object centre at (A) : 24.56000 20.42550 30.53500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4268847E-02 4.8085288E-03 midg,1,midg; midg,igrid,midg -1.5237286E-02 9.3193995E-03 1,midg,midg; igrid,midg,midg -1.4662871E-02 4.7256057E-03 gauss-seidel spectral radius is 0.9985088 estimated iterations to convergence 205 setup time was (sec) 0.9100000 now iterating at: 08:39:45 rms-change max change #iterations 4.230587 167.9637 at 10iterations 1.921230 74.83270 at 20iterations 0.8746482 29.21013 at 30iterations 0.3961625 11.57840 at 40iterations 0.1798586 5.686520 at 50iterations 8.1885904E-02 2.643995 at 60iterations 3.7437029E-02 1.186035 at 70iterations 1.7137447E-02 0.5175390 at 80iterations 7.9691764E-03 0.2491531 at 90iterations 3.8441599E-03 0.1266880 at 100iterations 1.9818756E-03 7.4577332E-02 at 110iterations 1.1164795E-03 4.2140961E-02 at 120iterations finished qdiffx linear iterations at : 08:39:52 total time elapsed so far: 7.620000 # loops : 120 mean,max change (kT/e) : 1.1164795E-03 4.2140961E-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) 7.810000 DelPhi exited at 08:39:53 7.812u 0.210s 0:08.69 92.2% 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 08:39:53 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3233 !!! WARNING: UMP 529 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.676513 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): 0.3460000 48.77400 ymin,ymax (A): -8.444000 49.29500 zmin,zma (A): 0.6079999 60.46200 x,y,z range (A): 48.42800 57.73900 59.85400 scale (grids/A): 2.676513 object centre (A): 24.56000 20.42550 30.53500 number of atom coordinates read : 3233 total number of charged atoms : 3088 net assigned charge : -1.099990 assigned positive charge : 486.5088 centred at (gu) : 88.88876 87.34234 94.99350 assigned negative charge : -487.6100 centred at (gu) : 88.41083 87.11868 94.64540 start vw surface at 0.1900000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 192872 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25721 grid for indexing accessible points = 1.400000 m= 102699 mr = 144882 m= 36609 mr = 86619 m= 7671 mr = 30211 m= 849 mr = 5838 m= 35 mr = 525 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.9400001 no. cavity mid-points inaccessible to solvent = 4062 time to turn everything in is 1.590000 number of dielectric boundary points 72647 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.730000 number of grid points assigned charge 24694 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) : 1.784342 object centre at (A) : 24.56000 20.42550 30.53500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3848628 -0.1347442 midg,1,midg; midg,igrid,midg -0.3413548 0.1599322 1,midg,midg; igrid,midg,midg -0.1811092 2.4906235E-02 gauss-seidel spectral radius is 0.9992325 estimated iterations to convergence 285 setup time was (sec) 1.900000 now iterating at: 08:39:55 rms-change max change #iterations 10.23576 278.1108 at 10iterations 5.948963 142.9725 at 20iterations 3.441219 70.73007 at 30iterations 1.975692 35.87616 at 40iterations 1.132837 21.07238 at 50iterations 0.6478996 11.82236 at 60iterations 0.3710888 7.154258 at 70iterations 0.2115542 4.555979 at 80iterations 0.1208194 2.113808 at 90iterations 6.9102637E-02 1.211959 at 100iterations 3.9408091E-02 0.6849380 at 110iterations 2.2472121E-02 0.4035912 at 120iterations 1.2880275E-02 0.2188835 at 130iterations 7.4309791E-03 0.1287575 at 140iterations 4.3377429E-03 7.9807281E-02 at 150iterations 2.5933667E-03 5.0127029E-02 at 160iterations 1.6186486E-03 3.2719612E-02 at 170iterations 1.0669722E-03 2.2672653E-02 at 180iterations finished qdiffx linear iterations at : 08:40:05 total time elapsed so far: 12.43000 # loops : 180 mean,max change (kT/e) : 1.0669722E-03 2.2672653E-02 energy calculations done at 12.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.62000 DelPhi exited at 08:40:06 12.620u 0.230s 0:13.50 95.1% 0+0k 0+0io 0pf+0w