Sat Oct 8 14:02:48 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 Sat Oct 8 2011 at 14:02:48 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2993 !!! WARNING: GLU 314 has a net charge of -0.2720 !!! WARNING: NDP 319 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6408179 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): -12.17600 43.37800 ymin,ymax (A): -23.89800 22.51800 zmin,zma (A): -6.577000 47.91600 x,y,z range (A): 55.55400 46.41600 54.49300 scale (grids/A): 0.6408179 object centre (A): 15.60100 -0.6899996 20.66950 number of atom coordinates read : 2993 total number of charged atoms : 2849 net assigned charge : 1.728008 assigned positive charge : 447.8306 centred at (gu) : 88.74739 90.08471 91.29412 assigned negative charge : -446.1033 centred at (gu) : 88.64164 89.94440 91.31737 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8165 nv = 96 ne = 84 npr = 62705 no. pairs analyzed = 62705 no. exposed pairs = 3359 no. arc points = 23764 no. surface atoms = 1153 nbur = 1840 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 411 mr = 4757 m= 0 mr = 43 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3776 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2324 ## 218 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9891 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.5562620E-09 -5.3410409E-10 midg,1,midg; midg,igrid,midg -1.6334486E-08 2.2100201E-08 1,midg,midg; igrid,midg,midg -1.5583204E-08 1.3072586E-08 gauss-seidel spectral radius is 0.9874123 estimated iterations to convergence 73 setup time was (sec) 0.6000000 now iterating at: 14:02:49 rms-change max change #iterations 0.1562917 18.98156 at 10iterations 1.6043160E-02 2.095053 at 20iterations 1.5878264E-03 0.2144146 at 30iterations 1.6858746E-04 2.2140503E-02 at 40iterations 1.8499439E-05 2.5939941E-03 at 50iterations finished qdiffx linear iterations at : 14:02:53 total time elapsed so far: 4.270000 # loops : 50 mean,max change (kT/e) : 1.8499439E-05 2.5939941E-03 energy calculations done at 4.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.440000 DelPhi exited at 14:02:54 4.447u 0.434s 0:05.18 94.0% 0+0k 0+0io 6pf+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 8 2011 at 14:02:54 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2993 !!! WARNING: GLU 314 has a net charge of -0.2720 !!! WARNING: NDP 319 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.922454 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): -12.17600 43.37800 ymin,ymax (A): -23.89800 22.51800 zmin,zma (A): -6.577000 47.91600 x,y,z range (A): 55.55400 46.41600 54.49300 scale (grids/A): 1.922454 object centre (A): 15.60100 -0.6899996 20.66950 number of atom coordinates read : 2993 total number of charged atoms : 2849 net assigned charge : 1.728008 assigned positive charge : 447.8306 centred at (gu) : 86.24149 90.25337 93.88202 assigned negative charge : -446.1033 centred at (gu) : 85.92440 89.83283 93.95204 start vw surface at 0.1300000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 88573 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23764 grid for indexing accessible points = 1.400000 m= 31552 mr = 63858 m= 4473 mr = 23592 m= 265 mr = 2681 m= 4 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7000000 number of dielectric boundary points 34644 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 155 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 22462 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) : 0.6408179 object centre at (A) : 15.60100 -0.6899996 20.66950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.7039301E-03 2.3700509E-03 midg,1,midg; midg,igrid,midg -4.7979360E-03 3.1051204E-02 1,midg,midg; igrid,midg,midg -3.8222127E-02 2.9560799E-02 gauss-seidel spectral radius is 0.9986920 estimated iterations to convergence 219 setup time was (sec) 1.060000 now iterating at: 14:02:55 rms-change max change #iterations 4.679031 185.6765 at 10iterations 2.236595 71.01837 at 20iterations 1.064234 32.09736 at 30iterations 0.5075554 15.24082 at 40iterations 0.2424008 7.019596 at 50iterations 0.1150952 3.348176 at 60iterations 5.4892436E-02 1.540433 at 70iterations 2.6225768E-02 0.7601166 at 80iterations 1.2447745E-02 0.3381672 at 90iterations 5.9511331E-03 0.1785755 at 100iterations 2.8290860E-03 8.3141327E-02 at 110iterations 1.3530082E-03 4.2469025E-02 at 120iterations finished qdiffx linear iterations at : 14:03:05 total time elapsed so far: 10.49000 # loops : 120 mean,max change (kT/e) : 1.3530082E-03 4.2469025E-02 energy calculations done at 10.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.65000 DelPhi exited at 14:03:05 10.656u 0.460s 0:11.36 97.7% 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 Sat Oct 8 2011 at 14:03:05 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2993 !!! WARNING: GLU 314 has a net charge of -0.2720 !!! WARNING: NDP 319 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.883681 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): -12.17600 43.37800 ymin,ymax (A): -23.89800 22.51800 zmin,zma (A): -6.577000 47.91600 x,y,z range (A): 55.55400 46.41600 54.49300 scale (grids/A): 2.883681 object centre (A): 15.60100 -0.6899996 20.66950 number of atom coordinates read : 2993 total number of charged atoms : 2849 net assigned charge : 1.728008 assigned positive charge : 447.8306 centred at (gu) : 84.36214 90.38010 95.82272 assigned negative charge : -446.1033 centred at (gu) : 83.88665 89.74909 95.92786 start vw surface at 0.1300000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 205358 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23764 grid for indexing accessible points = 1.400000 m= 103696 mr = 154156 m= 35699 mr = 86443 m= 7965 mr = 28627 m= 1121 mr = 5683 m= 62 mr = 724 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 1.110000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.850000 number of dielectric boundary points 78241 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.990000 number of grid points assigned charge 22792 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) : 1.922454 object centre at (A) : 15.60100 -0.6899996 20.66950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.5500485E-02 0.1673448 midg,1,midg; midg,igrid,midg -4.0596973E-02 0.3294367 1,midg,midg; igrid,midg,midg -0.5295467 0.3316163 gauss-seidel spectral radius is 0.9992768 estimated iterations to convergence 293 setup time was (sec) 2.180000 now iterating at: 14:03:08 rms-change max change #iterations 10.87420 409.9727 at 10iterations 6.367333 121.7654 at 20iterations 3.704988 80.00018 at 30iterations 2.154346 41.87270 at 40iterations 1.249239 22.29476 at 50iterations 0.7245577 12.06551 at 60iterations 0.4202852 6.986600 at 70iterations 0.2435453 4.205055 at 80iterations 0.1407849 2.363958 at 90iterations 8.1483774E-02 1.362190 at 100iterations 4.7095075E-02 0.8270321 at 110iterations 2.7236037E-02 0.4541266 at 120iterations 1.5771516E-02 0.2599867 at 130iterations 9.1228485E-03 0.1565304 at 140iterations 5.2753398E-03 8.6838722E-02 at 150iterations 3.0530468E-03 4.9826622E-02 at 160iterations 1.7666168E-03 3.0677795E-02 at 170iterations 1.0239840E-03 1.6342163E-02 at 180iterations finished qdiffx linear iterations at : 14:03:24 total time elapsed so far: 18.16000 # loops : 180 mean,max change (kT/e) : 1.0239840E-03 1.6342163E-02 energy calculations done at 18.16000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.32000 DelPhi exited at 14:03:24 18.328u 0.478s 0:19.07 98.5% 0+0k 0+0io 0pf+0w