Sat Oct 15 13:09:42 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 13:09:42 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3463 !!! WARNING: HIT 109 has a net charge of 0.5140 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: 0.5590979 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): 10.13200 73.80600 ymin,ymax (A): -25.89900 23.95400 zmin,zma (A): 27.83000 88.67400 x,y,z range (A): 63.67400 49.85300 60.84400 scale (grids/A): 0.5590979 object centre (A): 41.96900 -0.9724998 58.25200 number of atom coordinates read : 3463 total number of charged atoms : 3314 net assigned charge : 14.01402 assigned positive charge : 532.7443 centred at (gu) : 91.26061 91.84211 90.14546 assigned negative charge : -518.7319 centred at (gu) : 91.32376 91.74088 90.09049 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7197 nv = 96 ne = 84 npr = 66792 no. pairs analyzed = 66792 no. exposed pairs = 4625 no. arc points = 32950 no. surface atoms = 1542 nbur = 1921 mkacc time = 0.1100000 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= 303 mr = 3549 m= 1 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 3932 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3400 ## 443 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 9325 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.0547079E-10 2.1716766E-09 midg,1,midg; midg,igrid,midg 1.1026107E-10 4.1642370E-09 1,midg,midg; igrid,midg,midg 1.6304098E-09 8.2598595E-10 gauss-seidel spectral radius is 0.9835463 estimated iterations to convergence 64 setup time was (sec) 0.4600000 now iterating at: 13:09:42 rms-change max change #iterations 9.2486702E-02 13.96418 at 10iterations 6.6038505E-03 1.004395 at 20iterations 5.8034918E-04 9.0690613E-02 at 30iterations 1.3696204E-04 2.7352333E-02 at 40iterations 5.3211901E-05 1.1286974E-02 at 50iterations finished qdiffx linear iterations at : 13:09:47 total time elapsed so far: 3.440000 # loops : 50 mean,max change (kT/e) : 5.3211901E-05 1.1286974E-02 energy calculations done at 3.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 13:09:47 3.572u 0.211s 0:05.40 70.0% 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 15 2011 at 13:09:47 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3463 !!! WARNING: HIT 109 has a net charge of 0.5140 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: 1.677294 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): 10.13200 73.80600 ymin,ymax (A): -25.89900 23.95400 zmin,zma (A): 27.83000 88.67400 x,y,z range (A): 63.67400 49.85300 60.84400 scale (grids/A): 1.677294 object centre (A): 41.96900 -0.9724998 58.25200 number of atom coordinates read : 3463 total number of charged atoms : 3314 net assigned charge : 14.01402 assigned positive charge : 532.7443 centred at (gu) : 93.78088 95.52554 90.43537 assigned negative charge : -518.7319 centred at (gu) : 93.97080 95.22219 90.27114 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 79580 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32950 grid for indexing accessible points = 1.400000 m= 24342 mr = 52703 m= 2625 mr = 16527 m= 76 mr = 1267 m= 0 mr = 7 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 321 time to turn everything in is 0.3800000 number of dielectric boundary points 36119 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 393 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 25504 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) : 0.5590979 object centre at (A) : 41.96900 -0.9724998 58.25200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.0025814E-03 3.5231233E-02 midg,1,midg; midg,igrid,midg 6.3480036E-03 2.8814832E-02 1,midg,midg; igrid,midg,midg 1.7488658E-02 -2.3876237E-02 gauss-seidel spectral radius is 0.9983410 estimated iterations to convergence 195 setup time was (sec) 0.6100000 now iterating at: 13:09:48 rms-change max change #iterations 3.865426 176.4099 at 10iterations 1.670711 55.41745 at 20iterations 0.7223487 26.53954 at 30iterations 0.3109457 10.81611 at 40iterations 0.1350655 4.769416 at 50iterations 5.8410745E-02 1.913385 at 60iterations 2.5308972E-02 0.8780022 at 70iterations 1.0985979E-02 0.3541784 at 80iterations 4.7793454E-03 0.1549406 at 90iterations 2.0880653E-03 6.9944382E-02 at 100iterations 9.2223060E-04 3.2670975E-02 at 110iterations 4.2454229E-04 1.7040253E-02 at 120iterations finished qdiffx linear iterations at : 13:09:59 total time elapsed so far: 8.060000 # loops : 120 mean,max change (kT/e) : 4.2454229E-04 1.7040253E-02 energy calculations done at 8.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.200000 DelPhi exited at 13:09:59 8.200u 0.228s 0:12.07 69.7% 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 13:09:59 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3463 !!! WARNING: HIT 109 has a net charge of 0.5140 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: 2.515941 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): 10.13200 73.80600 ymin,ymax (A): -25.89900 23.95400 zmin,zma (A): 27.83000 88.67400 x,y,z range (A): 63.67400 49.85300 60.84400 scale (grids/A): 2.515941 object centre (A): 41.96900 -0.9724998 58.25200 number of atom coordinates read : 3463 total number of charged atoms : 3314 net assigned charge : 14.01402 assigned positive charge : 532.7443 centred at (gu) : 95.67097 98.28800 90.65282 assigned negative charge : -518.7319 centred at (gu) : 95.95605 97.83336 90.40658 start vw surface at 0.1000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 184616 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32950 grid for indexing accessible points = 1.400000 m= 84124 mr = 129157 m= 24259 mr = 65822 m= 4060 mr = 18083 m= 329 mr = 2630 m= 7 mr = 142 m= 0 mr = 2 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 1073 time to turn everything in is 0.9600000 number of dielectric boundary points 81559 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 26487 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) : 1.677294 object centre at (A) : 41.96900 -0.9724998 58.25200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8674186E-02 0.5370261 midg,1,midg; midg,igrid,midg 7.9821654E-02 0.4327791 1,midg,midg; igrid,midg,midg 0.1127761 -0.6353176 gauss-seidel spectral radius is 0.9992015 estimated iterations to convergence 279 setup time was (sec) 1.220000 now iterating at: 13:10:01 rms-change max change #iterations 9.815921 292.2369 at 10iterations 5.652277 132.3658 at 20iterations 3.240049 78.51970 at 30iterations 1.842610 41.07071 at 40iterations 1.046088 20.44772 at 50iterations 0.5917006 11.43090 at 60iterations 0.3344713 6.872437 at 70iterations 0.1890781 4.467773 at 80iterations 0.1067517 2.011215 at 90iterations 6.0155738E-02 1.151041 at 100iterations 3.3842638E-02 0.6433563 at 110iterations 1.9080585E-02 0.3847947 at 120iterations 1.0765461E-02 0.2027664 at 130iterations 6.0841218E-03 0.1287632 at 140iterations 3.4429266E-03 6.3347816E-02 at 150iterations 1.9678681E-03 4.5337200E-02 at 160iterations 1.1446960E-03 2.6748657E-02 at 170iterations 6.8584323E-04 1.5914917E-02 at 180iterations finished qdiffx linear iterations at : 13:10:13 total time elapsed so far: 13.19000 # loops : 180 mean,max change (kT/e) : 6.8584323E-04 1.5914917E-02 energy calculations done at 13.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.33000 DelPhi exited at 13:10:13 13.327u 0.247s 0:14.01 96.7% 0+0k 0+0io 0pf+0w