Tue Oct 11 06:04:10 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 06:04:10 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2277 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 0.7332345 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): 25.60600 72.09600 ymin,ymax (A): -18.51400 30.03800 zmin,zma (A): 4.296000 46.29000 x,y,z range (A): 46.49000 48.55200 41.99400 scale (grids/A): 0.7332345 object centre (A): 48.85100 5.762000 25.29300 number of atom coordinates read : 2277 total number of charged atoms : 1951 net assigned charge : 5.945010 assigned positive charge : 317.1460 centred at (gu) : 89.26479 90.37602 90.21291 assigned negative charge : -311.2011 centred at (gu) : 89.40379 90.30855 90.29243 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7684 nv = 96 ne = 84 npr = 41618 no. pairs analyzed = 41618 no. exposed pairs = 2555 no. arc points = 17401 no. surface atoms = 869 nbur = 1408 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 609 mr = 4539 m= 6 mr = 145 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3615 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1539 ## 153 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8245 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5111877E-07 2.1193525E-08 midg,1,midg; midg,igrid,midg 2.9262349E-08 1.5772942E-07 1,midg,midg; igrid,midg,midg 2.3822041E-07 -2.6770987E-08 gauss-seidel spectral radius is 0.9902993 estimated iterations to convergence 83 setup time was (sec) 0.5100000 now iterating at: 06:04:11 rms-change max change #iterations 0.2328338 33.15973 at 10iterations 3.1559192E-02 3.994598 at 20iterations 4.6320828E-03 0.6533203 at 30iterations 8.8076422E-04 0.1234493 at 40iterations 2.5393462E-04 2.8760910E-02 at 50iterations finished qdiffx linear iterations at : 06:04:14 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 2.5393462E-04 2.8760910E-02 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 06:04:14 3.399u 0.236s 0:04.01 90.2% 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 06:04:14 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2277 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.199703 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): 25.60600 72.09600 ymin,ymax (A): -18.51400 30.03800 zmin,zma (A): 4.296000 46.29000 x,y,z range (A): 46.49000 48.55200 41.99400 scale (grids/A): 2.199703 object centre (A): 48.85100 5.762000 25.29300 number of atom coordinates read : 2277 total number of charged atoms : 1951 net assigned charge : 5.945010 assigned positive charge : 317.1460 centred at (gu) : 87.79427 91.12824 90.63905 assigned negative charge : -311.2011 centred at (gu) : 88.21156 90.92548 90.87716 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 81680 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17401 grid for indexing accessible points = 1.400000 m= 34721 mr = 58706 m= 7515 mr = 26899 m= 831 mr = 5292 m= 26 mr = 434 m= 0 mr = 4 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6800000 number of dielectric boundary points 33438 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 63 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 15509 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) : 0.7332345 object centre at (A) : 48.85100 5.762000 25.29300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4009626E-02 3.0926475E-02 midg,1,midg; midg,igrid,midg 4.7026720E-02 3.1944897E-02 1,midg,midg; igrid,midg,midg 4.8730575E-02 -6.2219776E-02 gauss-seidel spectral radius is 0.9989015 estimated iterations to convergence 239 setup time was (sec) 0.9800000 now iterating at: 06:04:16 rms-change max change #iterations 4.899227 210.9532 at 10iterations 2.474518 77.81702 at 20iterations 1.260581 39.93381 at 30iterations 0.6369401 17.44482 at 40iterations 0.3227562 9.668118 at 50iterations 0.1644565 4.907112 at 60iterations 8.3415881E-02 2.320034 at 70iterations 4.2455722E-02 1.194466 at 80iterations 2.1675043E-02 0.5665865 at 90iterations 1.1182671E-02 0.3171387 at 100iterations 5.7696155E-03 0.1636543 at 110iterations 3.0524456E-03 8.9184761E-02 at 120iterations finished qdiffx linear iterations at : 06:04:22 total time elapsed so far: 7.080000 # loops : 120 mean,max change (kT/e) : 3.0524456E-03 8.9184761E-02 energy calculations done at 7.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.280000 DelPhi exited at 06:04:22 7.279u 0.229s 0:08.09 92.5% 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 06:04:23 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: 314 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2277 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 3.299555 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): 25.60600 72.09600 ymin,ymax (A): -18.51400 30.03800 zmin,zma (A): 4.296000 46.29000 x,y,z range (A): 46.49000 48.55200 41.99400 scale (grids/A): 3.299555 object centre (A): 48.85100 5.762000 25.29300 number of atom coordinates read : 2277 total number of charged atoms : 1951 net assigned charge : 5.945010 assigned positive charge : 317.1460 centred at (gu) : 86.69147 91.69234 90.95851 assigned negative charge : -311.2011 centred at (gu) : 87.31731 91.38818 91.31590 start vw surface at 0.1400000 fill in re-entrant regions at 0.8500000 boundary points on vw surface= 187799 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17401 grid for indexing accessible points = 1.400000 m= 105662 mr = 140568 m= 46121 mr = 88972 m= 14546 mr = 38645 m= 3333 mr = 11623 m= 439 mr = 2479 m= 23 mr = 283 m= 0 mr = 11 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.960000 number of dielectric boundary points 75342 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.100000 number of grid points assigned charge 15608 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) : 2.199703 object centre at (A) : 48.85100 5.762000 25.29300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.2761330E-02 0.2588589 midg,1,midg; midg,igrid,midg 0.3291411 0.1746243 1,midg,midg; igrid,midg,midg 0.4772241 -0.7208845 gauss-seidel spectral radius is 0.9993147 estimated iterations to convergence 301 setup time was (sec) 2.260000 now iterating at: 06:04:25 rms-change max change #iterations 10.74274 364.9594 at 10iterations 6.394984 114.7858 at 20iterations 3.801561 91.02097 at 30iterations 2.262841 41.62593 at 40iterations 1.342552 24.18928 at 50iterations 0.7939246 14.04331 at 60iterations 0.4706326 8.041986 at 70iterations 0.2781715 5.697308 at 80iterations 0.1643392 2.771000 at 90iterations 9.7227208E-02 1.600246 at 100iterations 5.7574563E-02 0.9216805 at 110iterations 3.4354772E-02 0.5812292 at 120iterations 2.0696659E-02 0.4185410 at 130iterations 1.2701232E-02 0.2332153 at 140iterations 8.0893189E-03 0.1385727 at 150iterations 5.3971959E-03 0.1011429 at 160iterations 3.8038574E-03 7.4638367E-02 at 170iterations 2.8554762E-03 5.0056458E-02 at 180iterations finished qdiffx linear iterations at : 06:04:35 total time elapsed so far: 12.46000 # loops : 180 mean,max change (kT/e) : 2.8554762E-03 5.0056458E-02 energy calculations done at 12.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.64000 DelPhi exited at 06:04:36 12.642u 0.216s 0:13.42 95.7% 0+0k 0+0io 0pf+0w