Sat Oct 15 11:28:03 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 15 2011 at 11:28:03 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3608 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: 0.5626502 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): -1.940000 60.03800 ymin,ymax (A): -18.31500 44.95700 zmin,zma (A): -5.269000 55.02800 x,y,z range (A): 61.97800 63.27200 60.29700 scale (grids/A): 0.5626502 object centre (A): 29.04900 13.32100 24.87950 number of atom coordinates read : 3608 total number of charged atoms : 3461 net assigned charge : -3.999971 assigned positive charge : 544.5237 centred at (gu) : 88.89637 86.27805 91.00618 assigned negative charge : -548.5258 centred at (gu) : 88.94608 86.21942 90.94809 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7491 nv = 96 ne = 84 npr = 72055 no. pairs analyzed = 72055 no. exposed pairs = 4650 no. arc points = 32590 no. surface atoms = 1560 nbur = 2048 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= 323 mr = 3907 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3885 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3363 ## 412 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 9783 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0234104E-09 5.2672505E-10 midg,1,midg; midg,igrid,midg -3.2793359E-09 1.6159425E-10 1,midg,midg; igrid,midg,midg 3.8082384E-10 -9.0459851E-10 gauss-seidel spectral radius is 0.9837558 estimated iterations to convergence 65 setup time was (sec) 0.4400000 now iterating at: 11:28:04 rms-change max change #iterations 9.4644256E-02 15.09170 at 10iterations 6.8793544E-03 1.261078 at 20iterations 5.7971763E-04 8.9848518E-02 at 30iterations 8.4758962E-05 1.7240047E-02 at 40iterations 2.1342956E-05 4.7132969E-03 at 50iterations finished qdiffx linear iterations at : 11:28:07 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 2.1342956E-05 4.7132969E-03 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 11:28:08 3.591u 0.207s 0:04.61 82.2% 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 Sat Oct 15 2011 at 11:28:08 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3608 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: 1.687951 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): -1.940000 60.03800 ymin,ymax (A): -18.31500 44.95700 zmin,zma (A): -5.269000 55.02800 x,y,z range (A): 61.97800 63.27200 60.29700 scale (grids/A): 1.687951 object centre (A): 29.04900 13.32100 24.87950 number of atom coordinates read : 3608 total number of charged atoms : 3461 net assigned charge : -3.999971 assigned positive charge : 544.5237 centred at (gu) : 86.68796 78.83299 93.01747 assigned negative charge : -548.5258 centred at (gu) : 86.83790 78.65774 92.84366 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 82719 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32590 grid for indexing accessible points = 1.400000 m= 26769 mr = 56649 m= 3081 mr = 18358 m= 93 mr = 1540 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.4000000 number of dielectric boundary points 36113 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 384 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 26747 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) : 0.5626502 object centre at (A) : 29.04900 13.32100 24.87950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.8681776E-04 4.9646893E-03 midg,1,midg; midg,igrid,midg -3.5891563E-02 2.0725369E-03 1,midg,midg; igrid,midg,midg -1.2930195E-02 -3.4562323E-02 gauss-seidel spectral radius is 0.9983587 estimated iterations to convergence 196 setup time was (sec) 0.6200000 now iterating at: 11:28:09 rms-change max change #iterations 3.994640 183.7247 at 10iterations 1.730432 56.60632 at 20iterations 0.7582900 25.09793 at 30iterations 0.3291786 11.83382 at 40iterations 0.1436167 4.438314 at 50iterations 6.2540933E-02 2.279613 at 60iterations 2.7242636E-02 0.9388857 at 70iterations 1.1884015E-02 0.3595276 at 80iterations 5.1871827E-03 0.1705437 at 90iterations 2.2679728E-03 7.0425510E-02 at 100iterations 9.9256006E-04 3.2994986E-02 at 110iterations 4.4124149E-04 1.4499664E-02 at 120iterations finished qdiffx linear iterations at : 11:28:16 total time elapsed so far: 8.160000 # loops : 120 mean,max change (kT/e) : 4.4124149E-04 1.4499664E-02 energy calculations done at 8.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.290000 DelPhi exited at 11:28:17 8.297u 0.256s 0:09.03 94.5% 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 Sat Oct 15 2011 at 11:28:17 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3608 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: 2.531926 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): -1.940000 60.03800 ymin,ymax (A): -18.31500 44.95700 zmin,zma (A): -5.269000 55.02800 x,y,z range (A): 61.97800 63.27200 60.29700 scale (grids/A): 2.531926 object centre (A): 29.04900 13.32100 24.87950 number of atom coordinates read : 3608 total number of charged atoms : 3461 net assigned charge : -3.999971 assigned positive charge : 544.5237 centred at (gu) : 85.03184 73.24944 94.52606 assigned negative charge : -548.5258 centred at (gu) : 85.25674 72.98639 94.26543 start vw surface at 0.1100000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 191977 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32590 grid for indexing accessible points = 1.400000 m= 91290 mr = 138232 m= 27180 mr = 72410 m= 4932 mr = 20353 m= 359 mr = 3157 m= 6 mr = 124 m= 0 mr = 0 time to grow re-entrant surface = 0.5700000 no. cavity mid-points inaccessible to solvent = 108 time to turn everything in is 1.040000 number of dielectric boundary points 81468 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 27660 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) : 1.687951 object centre at (A) : 29.04900 13.32100 24.87950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0144337E-03 0.2588196 midg,1,midg; midg,igrid,midg -0.5113907 1.7341183E-02 1,midg,midg; igrid,midg,midg -0.1894842 -0.6478699 gauss-seidel spectral radius is 0.9992056 estimated iterations to convergence 280 setup time was (sec) 1.280000 now iterating at: 11:28:18 rms-change max change #iterations 10.20112 329.7043 at 10iterations 5.868993 127.0013 at 20iterations 3.357087 84.51100 at 30iterations 1.914062 39.89986 at 40iterations 1.083683 22.64908 at 50iterations 0.6159599 11.83422 at 60iterations 0.3487278 6.775495 at 70iterations 0.1969563 3.728965 at 80iterations 0.1110900 2.090530 at 90iterations 6.2739350E-02 1.255522 at 100iterations 3.5382226E-02 0.6329947 at 110iterations 1.9959392E-02 0.3788919 at 120iterations 1.1253761E-02 0.2217249 at 130iterations 6.3548433E-03 0.1262455 at 140iterations 3.5779544E-03 6.5471649E-02 at 150iterations 2.0223053E-03 3.5725355E-02 at 160iterations 1.1437018E-03 2.0811081E-02 at 170iterations 6.5036392E-04 1.1352539E-02 at 180iterations finished qdiffx linear iterations at : 11:28:31 total time elapsed so far: 13.66000 # loops : 180 mean,max change (kT/e) : 6.5036392E-04 1.1352539E-02 energy calculations done at 13.66000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.79000 DelPhi exited at 11:28:31 13.792u 0.258s 0:14.38 97.6% 0+0k 0+0io 0pf+0w