Tue Oct 11 08:22:34 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 Tue Oct 11 2011 at 08:22:34 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3424 !!! WARNING: SEP 110 has a net charge of -0.4750 !!! WARNING: HIT 113 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5418487 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): 46.20700 101.9450 ymin,ymax (A): -1.297000 60.72400 zmin,zma (A): 56.52800 122.2290 x,y,z range (A): 55.73800 62.02100 65.70100 scale (grids/A): 0.5418487 object centre (A): 74.07600 29.71350 89.37850 number of atom coordinates read : 3424 total number of charged atoms : 3269 net assigned charge : 3.039020 assigned positive charge : 532.0005 centred at (gu) : 88.95071 89.86784 88.18778 assigned negative charge : -528.9631 centred at (gu) : 88.98502 89.96946 88.26501 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6498 nv = 96 ne = 84 npr = 65923 no. pairs analyzed = 65923 no. exposed pairs = 4893 no. arc points = 34495 no. surface atoms = 1627 nbur = 1797 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 = 1.596000 m= 276 mr = 2985 m= 0 mr = 4 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3785 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3501 ## 480 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 8620 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0468503E-09 -2.3840524E-10 midg,1,midg; midg,igrid,midg 8.4972518E-10 -5.2891830E-10 1,midg,midg; igrid,midg,midg 4.8922433E-10 -6.4432244E-11 gauss-seidel spectral radius is 0.9824868 estimated iterations to convergence 62 setup time was (sec) 0.4300000 now iterating at: 08:22:35 rms-change max change #iterations 7.9966217E-02 11.74428 at 10iterations 5.1860074E-03 0.8928223 at 20iterations 3.5060788E-04 5.4891586E-02 at 30iterations 3.4128036E-05 6.0386658E-03 at 40iterations 7.6646102E-06 1.5690327E-03 at 50iterations finished qdiffx linear iterations at : 08:22:38 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 7.6646102E-06 1.5690327E-03 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 08:22:38 3.464u 0.165s 0:04.24 85.3% 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 Tue Oct 11 2011 at 08:22:38 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3424 !!! WARNING: SEP 110 has a net charge of -0.4750 !!! WARNING: HIT 113 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.625546 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): 46.20700 101.9450 ymin,ymax (A): -1.297000 60.72400 zmin,zma (A): 56.52800 122.2290 x,y,z range (A): 55.73800 62.02100 65.70100 scale (grids/A): 1.625546 object centre (A): 74.07600 29.71350 89.37850 number of atom coordinates read : 3424 total number of charged atoms : 3269 net assigned charge : 3.039020 assigned positive charge : 532.0005 centred at (gu) : 86.85117 89.60286 84.56265 assigned negative charge : -528.9631 centred at (gu) : 86.95462 89.90796 84.79453 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 71108 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34495 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 21413 mr = 44676 m= 2294 mr = 13863 m= 54 mr = 1085 m= 0 mr = 2 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 282 time to turn everything in is 0.3600000 number of dielectric boundary points 35243 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 390 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 24975 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) : 0.5418487 object centre at (A) : 74.07600 29.71350 89.37850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1653957E-02 -7.1898178E-04 midg,1,midg; midg,igrid,midg -3.7148306E-03 -1.2113946E-02 1,midg,midg; igrid,midg,midg 1.0443475E-02 2.8136426E-03 gauss-seidel spectral radius is 0.9982295 estimated iterations to convergence 189 setup time was (sec) 0.5900000 now iterating at: 08:22:39 rms-change max change #iterations 3.676140 191.2438 at 10iterations 1.530988 59.78204 at 20iterations 0.6451420 23.62127 at 30iterations 0.2707950 9.855200 at 40iterations 0.1136050 4.301605 at 50iterations 4.7818180E-02 1.564047 at 60iterations 2.0015022E-02 0.6938248 at 70iterations 8.4402869E-03 0.3050919 at 80iterations 3.5563828E-03 0.1338081 at 90iterations 1.4941571E-03 5.0764561E-02 at 100iterations 6.3100213E-04 2.2808075E-02 at 110iterations 2.6542586E-04 8.6154938E-03 at 120iterations finished qdiffx linear iterations at : 08:22:47 total time elapsed so far: 7.830000 # loops : 120 mean,max change (kT/e) : 2.6542586E-04 8.6154938E-03 energy calculations done at 7.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.960000 DelPhi exited at 08:22:48 7.963u 0.227s 0:09.67 84.5% 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 08:22:48 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3424 !!! WARNING: SEP 110 has a net charge of -0.4750 !!! WARNING: HIT 113 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.438319 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): 46.20700 101.9450 ymin,ymax (A): -1.297000 60.72400 zmin,zma (A): 56.52800 122.2290 x,y,z range (A): 55.73800 62.02100 65.70100 scale (grids/A): 2.438319 object centre (A): 74.07600 29.71350 89.37850 number of atom coordinates read : 3424 total number of charged atoms : 3269 net assigned charge : 3.039020 assigned positive charge : 532.0005 centred at (gu) : 85.27651 89.40386 81.84377 assigned negative charge : -528.9631 centred at (gu) : 85.43171 89.86192 82.19170 start vw surface at 0.1000000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 164871 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34495 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 73225 mr = 110219 m= 21037 mr = 55582 m= 3477 mr = 15263 m= 269 mr = 2139 m= 5 mr = 122 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 884 time to turn everything in is 0.9000000 number of dielectric boundary points 79559 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 36 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 26126 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) : 1.625546 object centre at (A) : 74.07600 29.71350 89.37850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4604653E-03 5.0045244E-02 midg,1,midg; midg,igrid,midg -7.9282314E-02 -0.1843107 1,midg,midg; igrid,midg,midg 0.1527517 5.6836993E-02 gauss-seidel spectral radius is 0.9991705 estimated iterations to convergence 274 setup time was (sec) 1.150000 now iterating at: 08:22:49 rms-change max change #iterations 9.553841 326.7688 at 10iterations 5.487898 175.2298 at 20iterations 3.120541 79.86897 at 30iterations 1.765690 47.77559 at 40iterations 0.9960628 27.13414 at 50iterations 0.5599879 12.46957 at 60iterations 0.3143730 8.542155 at 70iterations 0.1758957 3.703365 at 80iterations 9.8462917E-02 2.205263 at 90iterations 5.4884229E-02 1.155374 at 100iterations 3.0656466E-02 0.6415672 at 110iterations 1.7032307E-02 0.3780160 at 120iterations 9.5283780E-03 0.2052231 at 130iterations 5.2943542E-03 0.1098623 at 140iterations 2.9470508E-03 5.8466434E-02 at 150iterations 1.6412715E-03 3.7652969E-02 at 160iterations 9.1255247E-04 1.8362045E-02 at 170iterations 5.0823105E-04 1.0759830E-02 at 180iterations finished qdiffx linear iterations at : 08:23:01 total time elapsed so far: 12.64000 # loops : 180 mean,max change (kT/e) : 5.0823105E-04 1.0759830E-02 energy calculations done at 12.64000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.77000 DelPhi exited at 08:23:02 12.770u 0.243s 0:14.03 92.7% 0+0k 0+0io 0pf+0w