Sat Oct 8 15:47:32 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 Sat Oct 8 2011 at 15:47:32 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2415 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 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: 0.6499078 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): -18.83100 29.57500 ymin,ymax (A): 36.97500 82.52600 zmin,zma (A): -18.97400 35.80300 x,y,z range (A): 48.40600 45.55100 54.77700 scale (grids/A): 0.6499078 object centre (A): 5.372000 59.75050 8.414499 number of atom coordinates read : 2415 total number of charged atoms : 2345 net assigned charge : 4.806003 assigned positive charge : 361.4479 centred at (gu) : 89.09344 91.08442 90.50486 assigned negative charge : -356.6427 centred at (gu) : 89.04161 90.98203 90.52870 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6894 nv = 96 ne = 84 npr = 48321 no. pairs analyzed = 48321 no. exposed pairs = 2996 no. arc points = 20812 no. surface atoms = 1021 nbur = 1394 mkacc time = 0.1800000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 405 mr = 3823 m= 3 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.3900000 number of dielectric boundary points 3413 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2036 ## 192 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 8285 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1254919E-08 6.4430998E-09 midg,1,midg; midg,igrid,midg -4.0914485E-09 2.9325653E-08 1,midg,midg; igrid,midg,midg 2.1842768E-09 1.3556705E-08 gauss-seidel spectral radius is 0.9877166 estimated iterations to convergence 74 setup time was (sec) 0.6800000 now iterating at: 15:47:33 rms-change max change #iterations 0.1499461 21.01774 at 10iterations 1.5423414E-02 2.118160 at 20iterations 1.5865471E-03 0.2154865 at 30iterations 1.7466489E-04 2.6306152E-02 at 40iterations 2.2632979E-05 3.4708977E-03 at 50iterations finished qdiffx linear iterations at : 15:47:37 total time elapsed so far: 4.360000 # loops : 50 mean,max change (kT/e) : 2.2632979E-05 3.4708977E-03 energy calculations done at 4.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.580000 DelPhi exited at 15:47:37 4.583u 0.425s 0:05.26 95.0% 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 15:47:37 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2415 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 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: 1.949724 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): -18.83100 29.57500 ymin,ymax (A): 36.97500 82.52600 zmin,zma (A): -18.97400 35.80300 x,y,z range (A): 48.40600 45.55100 54.77700 scale (grids/A): 1.949724 object centre (A): 5.372000 59.75050 8.414499 number of atom coordinates read : 2415 total number of charged atoms : 2345 net assigned charge : 4.806003 assigned positive charge : 361.4479 centred at (gu) : 87.27951 93.25253 91.51434 assigned negative charge : -356.6427 centred at (gu) : 87.12481 92.94584 91.58599 start vw surface at 0.1500000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 74415 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20812 grid for indexing accessible points = 1.400000 m= 27859 mr = 52056 m= 5046 mr = 20674 m= 345 mr = 3439 m= 2 mr = 153 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 908 time to turn everything in is 0.7600000 number of dielectric boundary points 31345 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 103 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 18473 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) : 0.6499078 object centre at (A) : 5.372000 59.75050 8.414499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6471509E-02 2.8240609E-03 midg,1,midg; midg,igrid,midg -4.0031685E-03 2.5197016E-02 1,midg,midg; igrid,midg,midg -3.3220079E-02 1.1259352E-02 gauss-seidel spectral radius is 0.9986776 estimated iterations to convergence 218 setup time was (sec) 1.100000 now iterating at: 15:47:39 rms-change max change #iterations 4.278558 224.9230 at 10iterations 2.028105 78.73421 at 20iterations 0.9590135 33.41664 at 30iterations 0.4567244 15.16602 at 40iterations 0.2165986 6.388110 at 50iterations 0.1029755 3.022797 at 60iterations 4.8836820E-02 1.841305 at 70iterations 2.3155086E-02 0.7007618 at 80iterations 1.1004998E-02 0.3601151 at 90iterations 5.2190507E-03 0.1570587 at 100iterations 2.4839875E-03 7.4365258E-02 at 110iterations 1.1820836E-03 3.6548436E-02 at 120iterations finished qdiffx linear iterations at : 15:47:48 total time elapsed so far: 10.42000 # loops : 120 mean,max change (kT/e) : 1.1820836E-03 3.6548436E-02 energy calculations done at 10.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.62000 DelPhi exited at 15:47:48 10.629u 0.445s 0:11.38 97.1% 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 15:47:49 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2415 !!! WARNING: ASL 705 has a net charge of -0.1000 !!! WARNING: GLM 711 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: 2.924585 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): -18.83100 29.57500 ymin,ymax (A): 36.97500 82.52600 zmin,zma (A): -18.97400 35.80300 x,y,z range (A): 48.40600 45.55100 54.77700 scale (grids/A): 2.924585 object centre (A): 5.372000 59.75050 8.414499 number of atom coordinates read : 2415 total number of charged atoms : 2345 net assigned charge : 4.806003 assigned positive charge : 361.4479 centred at (gu) : 85.91912 94.87868 92.27135 assigned negative charge : -356.6427 centred at (gu) : 85.68721 94.41882 92.37897 start vw surface at 0.1600000 fill in re-entrant regions at 0.6600000 boundary points on vw surface= 172156 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20812 grid for indexing accessible points = 1.400000 m= 88535 mr = 126095 m= 34035 mr = 72571 m= 9418 mr = 27741 m= 1551 mr = 7392 m= 106 mr = 1144 m= 2 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 1.210000 no. cavity mid-points inaccessible to solvent = 2941 time to turn everything in is 2.010000 number of dielectric boundary points 70798 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.160000 number of grid points assigned charge 18759 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) : 1.949724 object centre at (A) : 5.372000 59.75050 8.414499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2222939 -7.2146520E-02 midg,1,midg; midg,igrid,midg -7.7605814E-02 0.1847081 1,midg,midg; igrid,midg,midg -0.3823654 0.1018020 gauss-seidel spectral radius is 0.9992684 estimated iterations to convergence 292 setup time was (sec) 2.380000 now iterating at: 15:47:51 rms-change max change #iterations 9.928862 534.7935 at 10iterations 5.822418 140.7845 at 20iterations 3.392453 68.05157 at 30iterations 1.980009 41.43035 at 40iterations 1.150273 19.95289 at 50iterations 0.6692530 12.80949 at 60iterations 0.3871863 7.389956 at 70iterations 0.2242533 4.637863 at 80iterations 0.1294588 2.387781 at 90iterations 7.4786313E-02 1.380757 at 100iterations 4.3278292E-02 0.8009300 at 110iterations 2.5020832E-02 0.4735832 at 120iterations 1.4401541E-02 0.2644043 at 130iterations 8.3254548E-03 0.1608849 at 140iterations 4.8084389E-03 8.5660934E-02 at 150iterations 2.7652027E-03 4.7731400E-02 at 160iterations 1.5987097E-03 2.8820038E-02 at 170iterations 9.2267361E-04 1.6555786E-02 at 180iterations finished qdiffx linear iterations at : 15:48:07 total time elapsed so far: 17.58000 # loops : 180 mean,max change (kT/e) : 9.2267361E-04 1.6555786E-02 energy calculations done at 17.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.81000 DelPhi exited at 15:48:07 17.810u 0.441s 0:18.52 98.5% 0+0k 0+0io 0pf+0w