Mon Oct 10 14:02:32 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 Mon Oct 10 2011 at 14:02:33 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3503 !!! WARNING: ASL 38 has a net charge of -0.1000 !!! WARNING: GLM 44 has a net charge of -0.0940 !!! WARNING: GLM 116 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: 0.5686265 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): 14.68000 68.47900 ymin,ymax (A): -20.38200 42.22500 zmin,zma (A): -28.52000 33.46900 x,y,z range (A): 53.79900 62.60700 61.98900 scale (grids/A): 0.5686265 object centre (A): 41.57950 10.92150 2.474501 number of atom coordinates read : 3503 total number of charged atoms : 3370 net assigned charge : 2.212007 assigned positive charge : 527.4947 centred at (gu) : 89.15366 89.09509 89.89027 assigned negative charge : -525.2848 centred at (gu) : 89.25747 89.09567 89.81392 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7413 nv = 96 ne = 84 npr = 66856 no. pairs analyzed = 66856 no. exposed pairs = 5390 no. arc points = 38798 no. surface atoms = 1752 nbur = 1751 mkacc time = 0.1200000 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 = 1.512000 m= 365 mr = 3111 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 4649 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3772 ## 422 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 9628 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0845139E-09 1.6035844E-09 midg,1,midg; midg,igrid,midg 3.9273174E-10 2.4191013E-10 1,midg,midg; igrid,midg,midg 2.6044222E-09 -1.2624914E-09 gauss-seidel spectral radius is 0.9841045 estimated iterations to convergence 65 setup time was (sec) 0.4500000 now iterating at: 14:02:33 rms-change max change #iterations 9.8097458E-02 16.30444 at 10iterations 7.1619237E-03 1.058153 at 20iterations 5.8149395E-04 8.2490444E-02 at 30iterations 9.3258430E-05 1.3295174E-02 at 40iterations 2.8153223E-05 3.7226677E-03 at 50iterations finished qdiffx linear iterations at : 14:02:36 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 2.8153223E-05 3.7226677E-03 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 14:02:36 3.419u 0.163s 0:03.93 90.8% 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 Oct 10 2011 at 14:02:37 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3503 !!! WARNING: ASL 38 has a net charge of -0.1000 !!! WARNING: GLM 44 has a net charge of -0.0940 !!! WARNING: GLM 116 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: 1.705879 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): 14.68000 68.47900 ymin,ymax (A): -20.38200 42.22500 zmin,zma (A): -28.52000 33.46900 x,y,z range (A): 53.79900 62.60700 61.98900 scale (grids/A): 1.705879 object centre (A): 41.57950 10.92150 2.474501 number of atom coordinates read : 3503 total number of charged atoms : 3370 net assigned charge : 2.212007 assigned positive charge : 527.4947 centred at (gu) : 87.46012 87.28408 89.66973 assigned negative charge : -525.2848 centred at (gu) : 87.77239 87.28664 89.44144 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 79531 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38798 grid for indexing accessible points = 1.400000 m= 24343 mr = 47620 m= 3279 mr = 14901 m= 169 mr = 1686 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 52 time to turn everything in is 0.4100000 number of dielectric boundary points 43091 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 295 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 26066 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) : 0.5686265 object centre at (A) : 41.57950 10.92150 2.474501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2783913E-02 1.7152490E-02 midg,1,midg; midg,igrid,midg -8.8484343E-03 1.3338240E-02 1,midg,midg; igrid,midg,midg 1.4099284E-02 -6.5833060E-03 gauss-seidel spectral radius is 0.9984300 estimated iterations to convergence 200 setup time was (sec) 0.6600000 now iterating at: 14:02:37 rms-change max change #iterations 4.044418 154.9859 at 10iterations 1.790015 60.41999 at 20iterations 0.7864801 27.79033 at 30iterations 0.3491264 12.25876 at 40iterations 0.1534657 5.079661 at 50iterations 6.7832924E-02 2.427866 at 60iterations 3.0107714E-02 1.154494 at 70iterations 1.3295355E-02 0.4399059 at 80iterations 5.9061744E-03 0.2029648 at 90iterations 2.6261271E-03 8.3889008E-02 at 100iterations 1.1816180E-03 3.9539337E-02 at 110iterations 5.3755782E-04 1.8352509E-02 at 120iterations finished qdiffx linear iterations at : 14:02:45 total time elapsed so far: 8.620000 # loops : 120 mean,max change (kT/e) : 5.3755782E-04 1.8352509E-02 energy calculations done at 8.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.750000 DelPhi exited at 14:02:46 8.753u 0.260s 0:09.81 91.8% 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 Oct 10 2011 at 14:02:46 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3503 !!! WARNING: ASL 38 has a net charge of -0.1000 !!! WARNING: GLM 44 has a net charge of -0.0940 !!! WARNING: GLM 116 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: 2.558819 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): 14.68000 68.47900 ymin,ymax (A): -20.38200 42.22500 zmin,zma (A): -28.52000 33.46900 x,y,z range (A): 53.79900 62.60700 61.98900 scale (grids/A): 2.558819 object centre (A): 41.57950 10.92150 2.474501 number of atom coordinates read : 3503 total number of charged atoms : 3370 net assigned charge : 2.212007 assigned positive charge : 527.4947 centred at (gu) : 86.18979 85.92577 89.50426 assigned negative charge : -525.2848 centred at (gu) : 86.65852 85.93005 89.16212 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 184243 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38798 grid for indexing accessible points = 1.400000 m= 80058 mr = 118462 m= 25495 mr = 58234 m= 5410 mr = 17875 m= 646 mr = 3603 m= 21 mr = 359 m= 0 mr = 6 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 106 time to turn everything in is 0.9900000 number of dielectric boundary points 97334 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 26945 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) : 1.705879 object centre at (A) : 41.57950 10.92150 2.474501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1481602 0.2231229 midg,1,midg; midg,igrid,midg -0.1594127 0.1593326 1,midg,midg; igrid,midg,midg 0.1682034 -0.1410379 gauss-seidel spectral radius is 0.9992464 estimated iterations to convergence 288 setup time was (sec) 1.250000 now iterating at: 14:02:48 rms-change max change #iterations 10.47097 294.4482 at 10iterations 6.230835 158.6549 at 20iterations 3.678553 93.42610 at 30iterations 2.157566 52.67257 at 40iterations 1.257712 30.23931 at 50iterations 0.7301236 16.24921 at 60iterations 0.4237565 9.570775 at 70iterations 0.2440790 5.788630 at 80iterations 0.1409879 2.857885 at 90iterations 8.1054524E-02 1.775546 at 100iterations 4.6685271E-02 0.9430008 at 110iterations 2.6843272E-02 0.5415154 at 120iterations 1.5374950E-02 0.2848743 at 130iterations 8.8305539E-03 0.1658392 at 140iterations 5.0626085E-03 9.7042084E-02 at 150iterations 2.9035753E-03 5.4123878E-02 at 160iterations 1.6659106E-03 2.9234886E-02 at 170iterations 9.5598103E-04 1.8112183E-02 at 180iterations finished qdiffx linear iterations at : 14:02:59 total time elapsed so far: 12.79000 # loops : 180 mean,max change (kT/e) : 9.5598103E-04 1.8112183E-02 energy calculations done at 12.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.91000 DelPhi exited at 14:03:00 12.916u 0.227s 0:13.75 95.4% 0+0k 0+0io 0pf+0w