Mon Feb 6 00:57:54 PST 2012 #!/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 Feb 6 2012 at 00:57:54 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 ! Automatically converted by prot2crg.py # of charge parameter records: 968 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2731 !!! WARNING: ADP 662 has a net charge of -2.0000 !!! WARNING: MG 664 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5928887 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): -7.958000 52.08700 ymin,ymax (A): -16.17900 34.45800 zmin,zma (A): 77.38900 129.9400 x,y,z range (A): 60.04500 50.63700 52.55100 scale (grids/A): 0.5928887 object centre (A): 22.06450 9.139500 103.6645 number of atom coordinates read : 2731 total number of charged atoms : 2589 net assigned charge : -4.999992 assigned positive charge : 423.9495 centred at (gu) : 92.02133 89.63910 89.41039 assigned negative charge : -428.9503 centred at (gu) : 91.97669 89.73955 89.51731 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6419 nv = 96 ne = 84 npr = 54056 no. pairs analyzed = 54056 no. exposed pairs = 3664 no. arc points = 25347 no. surface atoms = 1225 nbur = 1506 mkacc time = 8.9999996E-02 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 = 1.484000 m= 323 mr = 3335 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3384 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2629 ## 315 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 8031 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8979402E-09 -4.5672772E-09 midg,1,midg; midg,igrid,midg 1.5729577E-09 -4.6168767E-09 1,midg,midg; igrid,midg,midg -2.0263125E-09 -4.5770190E-10 gauss-seidel spectral radius is 0.9852948 estimated iterations to convergence 68 setup time was (sec) 0.4200000 now iterating at: 00:57:56 rms-change max change #iterations 0.1109676 18.84407 at 10iterations 9.1462573E-03 1.553719 at 20iterations 7.5229281E-04 0.1349297 at 30iterations 6.7870671E-05 1.0853291E-02 at 40iterations 9.6242338E-06 1.5449524E-03 at 50iterations finished qdiffx linear iterations at : 00:57:59 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 9.6242338E-06 1.5449524E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 00:58:00 3.465u 0.163s 0:05.58 64.8% 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 Mon Feb 6 2012 at 00:58:00 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 ! Automatically converted by prot2crg.py # of charge parameter records: 968 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2731 !!! WARNING: ADP 662 has a net charge of -2.0000 !!! WARNING: MG 664 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.778666 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): -7.958000 52.08700 ymin,ymax (A): -16.17900 34.45800 zmin,zma (A): 77.38900 129.9400 x,y,z range (A): 60.04500 50.63700 52.55100 scale (grids/A): 1.778666 object centre (A): 22.06450 9.139500 103.6645 number of atom coordinates read : 2731 total number of charged atoms : 2589 net assigned charge : -4.999992 assigned positive charge : 423.9495 centred at (gu) : 96.06343 88.91666 88.23063 assigned negative charge : -428.9503 centred at (gu) : 95.92982 89.21839 88.55180 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 69749 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25347 grid for indexing accessible points = 1.400000 m= 23454 mr = 47033 m= 3205 mr = 16256 m= 152 mr = 1747 m= 2 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 31497 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 269 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 20250 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) : 0.5928887 object centre at (A) : 22.06450 9.139500 103.6645 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.6958950E-03 -3.5746653E-02 midg,1,midg; midg,igrid,midg -9.7964657E-03 -2.0138806E-02 1,midg,midg; igrid,midg,midg 2.0765716E-02 2.7627759E-02 gauss-seidel spectral radius is 0.9984606 estimated iterations to convergence 202 setup time was (sec) 0.5800000 now iterating at: 00:58:01 rms-change max change #iterations 3.933384 192.1714 at 10iterations 1.755712 72.54556 at 20iterations 0.7784341 27.17162 at 30iterations 0.3487681 11.83931 at 40iterations 0.1551886 5.452535 at 50iterations 6.9337323E-02 2.184292 at 60iterations 3.1113395E-02 0.9959431 at 70iterations 1.3886921E-02 0.5058670 at 80iterations 6.1903084E-03 0.1952152 at 90iterations 2.7759895E-03 0.1067526 at 100iterations 1.2461483E-03 4.3930054E-02 at 110iterations 5.5992760E-04 1.8723339E-02 at 120iterations finished qdiffx linear iterations at : 00:58:08 total time elapsed so far: 7.690000 # loops : 120 mean,max change (kT/e) : 5.5992760E-04 1.8723339E-02 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 00:58:09 7.816u 0.206s 0:08.87 90.3% 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 Mon Feb 6 2012 at 00:58:09 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 ! Automatically converted by prot2crg.py # of charge parameter records: 968 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2731 !!! WARNING: ADP 662 has a net charge of -2.0000 !!! WARNING: MG 664 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.667999 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): -7.958000 52.08700 ymin,ymax (A): -16.17900 34.45800 zmin,zma (A): 77.38900 129.9400 x,y,z range (A): 60.04500 50.63700 52.55100 scale (grids/A): 2.667999 object centre (A): 22.06450 9.139500 103.6645 number of atom coordinates read : 2731 total number of charged atoms : 2589 net assigned charge : -4.999992 assigned positive charge : 423.9495 centred at (gu) : 99.09495 88.37488 87.34586 assigned negative charge : -428.9503 centred at (gu) : 98.89467 88.82753 87.82750 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 161524 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25347 grid for indexing accessible points = 1.400000 m= 77799 mr = 114719 m= 25399 mr = 61542 m= 5439 mr = 19462 m= 607 mr = 3741 m= 20 mr = 339 m= 0 mr = 1 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8600000 number of dielectric boundary points 70984 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 20709 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) : 1.778666 object centre at (A) : 22.06450 9.139500 103.6645 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.8906715E-02 -0.4671729 midg,1,midg; midg,igrid,midg -0.1436770 -0.2065867 1,midg,midg; igrid,midg,midg 0.4247123 0.2365749 gauss-seidel spectral radius is 0.9992170 estimated iterations to convergence 282 setup time was (sec) 1.100000 now iterating at: 00:58:10 rms-change max change #iterations 9.751375 269.8148 at 10iterations 5.643781 130.1214 at 20iterations 3.238598 74.18027 at 30iterations 1.854512 39.01554 at 40iterations 1.057729 22.84399 at 50iterations 0.6010313 12.67109 at 60iterations 0.3416781 6.919099 at 70iterations 0.1939045 3.905464 at 80iterations 0.1097830 2.096457 at 90iterations 6.2160365E-02 1.252121 at 100iterations 3.5343759E-02 0.7182646 at 110iterations 1.9947900E-02 0.3834667 at 120iterations 1.1274544E-02 0.2298999 at 130iterations 6.3853813E-03 0.1277304 at 140iterations 3.6070752E-03 7.2677612E-02 at 150iterations 2.0411860E-03 4.0863037E-02 at 160iterations 1.1578575E-03 2.1461725E-02 at 170iterations 6.5503450E-04 1.3267517E-02 at 180iterations finished qdiffx linear iterations at : 00:58:22 total time elapsed so far: 12.48000 # loops : 180 mean,max change (kT/e) : 6.5503450E-04 1.3267517E-02 energy calculations done at 12.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.60000 DelPhi exited at 00:58:22 12.607u 0.232s 0:13.32 96.3% 0+0k 0+0io 0pf+0w