Tue Oct 11 06:16:18 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+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 Tue Oct 11 2011 at 06:16:18 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2009 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: 0.7230923 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): -19.71200 24.11100 ymin,ymax (A): -9.988999 28.64600 zmin,zma (A): -3.488000 45.74500 x,y,z range (A): 43.82300 38.63500 49.23300 scale (grids/A): 0.7230923 object centre (A): 2.199500 9.328501 21.12850 number of atom coordinates read : 2009 total number of charged atoms : 1881 net assigned charge : 6.500006 assigned positive charge : 303.9531 centred at (gu) : 89.95629 89.01817 91.25688 assigned negative charge : -297.4532 centred at (gu) : 89.80497 89.05345 91.33230 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7262 nv = 96 ne = 84 npr = 39634 no. pairs analyzed = 39634 no. exposed pairs = 2551 no. arc points = 17526 no. surface atoms = 859 nbur = 1150 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 568 mr = 4142 m= 1 mr = 109 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 0.3100000 number of dielectric boundary points 3580 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1523 ## 143 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7727 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0176054E-07 3.5545114E-08 midg,1,midg; midg,igrid,midg 1.2324678E-07 4.6821174E-08 1,midg,midg; igrid,midg,midg -2.2678419E-08 1.7641241E-07 gauss-seidel spectral radius is 0.9900233 estimated iterations to convergence 81 setup time was (sec) 0.6100000 now iterating at: 06:16:19 rms-change max change #iterations 0.2114090 40.30576 at 10iterations 2.7597440E-02 3.412797 at 20iterations 3.6392952E-03 0.5218811 at 30iterations 5.5862108E-04 7.9059601E-02 at 40iterations 1.2124199E-04 1.7227173E-02 at 50iterations finished qdiffx linear iterations at : 06:16:23 total time elapsed so far: 4.170000 # loops : 50 mean,max change (kT/e) : 1.2124199E-04 1.7227173E-02 energy calculations done at 4.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.410000 DelPhi exited at 06:16:24 4.410u 0.400s 0:05.24 91.7% 0+0k 0+0io 4pf+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 06:16:24 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2009 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: 2.169277 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): -19.71200 24.11100 ymin,ymax (A): -9.988999 28.64600 zmin,zma (A): -3.488000 45.74500 x,y,z range (A): 43.82300 38.63500 49.23300 scale (grids/A): 2.169277 object centre (A): 2.199500 9.328501 21.12850 number of atom coordinates read : 2009 total number of charged atoms : 1881 net assigned charge : 6.500006 assigned positive charge : 303.9531 centred at (gu) : 89.86903 87.05466 93.77061 assigned negative charge : -297.4532 centred at (gu) : 89.41508 87.16063 93.99694 start vw surface at 0.1400000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 76461 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17526 grid for indexing accessible points = 1.400000 m= 32011 mr = 53772 m= 6924 mr = 24292 m= 724 mr = 4713 m= 20 mr = 372 m= 0 mr = 2 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8200000 number of dielectric boundary points 32989 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 42 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 14946 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) : 0.7230923 object centre at (A) : 2.199500 9.328501 21.12850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5622793E-02 1.2318964E-02 midg,1,midg; midg,igrid,midg 4.1386951E-02 7.7629872E-03 1,midg,midg; igrid,midg,midg 2.8728250E-02 4.9925666E-02 gauss-seidel spectral radius is 0.9988714 estimated iterations to convergence 236 setup time was (sec) 1.160000 now iterating at: 06:16:25 rms-change max change #iterations 4.668866 190.7516 at 10iterations 2.341526 72.21387 at 20iterations 1.181148 35.65696 at 30iterations 0.5938520 17.58828 at 40iterations 0.2990280 9.411751 at 50iterations 0.1501475 4.577043 at 60iterations 7.5585820E-02 2.378127 at 70iterations 3.8083702E-02 1.129475 at 80iterations 1.9109298E-02 0.5663264 at 90iterations 9.6402429E-03 0.2683945 at 100iterations 4.8602307E-03 0.1499808 at 110iterations 2.4757439E-03 7.2170258E-02 at 120iterations finished qdiffx linear iterations at : 06:16:34 total time elapsed so far: 10.38000 # loops : 120 mean,max change (kT/e) : 2.4757439E-03 7.2170258E-02 energy calculations done at 10.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.60000 DelPhi exited at 06:16:35 10.608u 0.472s 0:11.53 96.0% 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 Tue Oct 11 2011 at 06:16:35 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2009 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: 3.253915 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): -19.71200 24.11100 ymin,ymax (A): -9.988999 28.64600 zmin,zma (A): -3.488000 45.74500 x,y,z range (A): 43.82300 38.63500 49.23300 scale (grids/A): 3.253915 object centre (A): 2.199500 9.328501 21.12850 number of atom coordinates read : 2009 total number of charged atoms : 1881 net assigned charge : 6.500006 assigned positive charge : 303.9531 centred at (gu) : 89.80350 85.58186 95.65589 assigned negative charge : -297.4532 centred at (gu) : 89.12269 85.74097 95.99548 start vw surface at 0.1300000 fill in re-entrant regions at 0.9900000 boundary points on vw surface= 175946 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17526 grid for indexing accessible points = 1.400000 m= 97480 mr = 129500 m= 42133 mr = 80833 m= 13322 mr = 34855 m= 2918 mr = 10365 m= 388 mr = 2097 m= 13 mr = 250 m= 0 mr = 4 time to grow re-entrant surface = 1.390000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.510000 number of dielectric boundary points 74296 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.660000 number of grid points assigned charge 15040 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) : 2.169277 object centre at (A) : 2.199500 9.328501 21.12850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1022506 2.9120881E-02 midg,1,midg; midg,igrid,midg 0.3319211 3.8485300E-02 1,midg,midg; igrid,midg,midg 0.4664404 0.4137906 gauss-seidel spectral radius is 0.9993075 estimated iterations to convergence 300 setup time was (sec) 2.860000 now iterating at: 06:16:39 rms-change max change #iterations 10.34686 317.0656 at 10iterations 6.198985 138.7596 at 20iterations 3.689739 86.83671 at 30iterations 2.194720 43.15995 at 40iterations 1.301966 27.82914 at 50iterations 0.7701689 13.72157 at 60iterations 0.4551810 8.334699 at 70iterations 0.2685605 5.506139 at 80iterations 0.1581844 2.826829 at 90iterations 9.3201689E-02 1.696841 at 100iterations 5.4972135E-02 0.9785528 at 110iterations 3.2482211E-02 0.5642166 at 120iterations 1.9203179E-02 0.3341560 at 130iterations 1.1475068E-02 0.2108059 at 140iterations 6.9479179E-03 0.1217449 at 150iterations 4.3163328E-03 7.3896885E-02 at 160iterations 2.7824244E-03 4.5103073E-02 at 170iterations 1.8988043E-03 3.3288956E-02 at 180iterations finished qdiffx linear iterations at : 06:16:54 total time elapsed so far: 18.14000 # loops : 180 mean,max change (kT/e) : 1.8988043E-03 3.3288956E-02 energy calculations done at 18.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.36000 DelPhi exited at 06:16:55 18.361u 0.511s 0:19.24 98.0% 0+0k 0+0io 0pf+0w