Mon Oct 10 17:13:08 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 17:13:08 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2996 !!! WARNING: HIT 107 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6156826 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): 14.73000 72.55200 ymin,ymax (A): 3.127000 53.04500 zmin,zma (A): 6.160000 63.70200 x,y,z range (A): 57.82200 49.91800 57.54200 scale (grids/A): 0.6156826 object centre (A): 43.64100 28.08600 34.93100 number of atom coordinates read : 2996 total number of charged atoms : 2854 net assigned charge : -4.485965 assigned positive charge : 453.6037 centred at (gu) : 89.01962 90.58686 91.62205 assigned negative charge : -458.0911 centred at (gu) : 88.97813 90.67544 91.73202 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7598 nv = 96 ne = 84 npr = 59930 no. pairs analyzed = 59930 no. exposed pairs = 3938 no. arc points = 28312 no. surface atoms = 1342 nbur = 1654 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 403 mr = 3948 m= 2 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 21 time to turn everything in is 0.3300000 number of dielectric boundary points 4007 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2773 ## 274 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9404 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.1199485E-09 -1.5258795E-08 midg,1,midg; midg,igrid,midg 2.7005136E-09 -1.0359447E-08 1,midg,midg; igrid,midg,midg -7.2039792E-09 -1.0131350E-10 gauss-seidel spectral radius is 0.9863822 estimated iterations to convergence 70 setup time was (sec) 0.5500000 now iterating at: 17:13:08 rms-change max change #iterations 0.1343569 18.44098 at 10iterations 1.2032508E-02 1.624710 at 20iterations 1.0961662E-03 0.1728821 at 30iterations 1.0046711E-04 1.4721394E-02 at 40iterations 9.6893054E-06 1.3923645E-03 at 50iterations finished qdiffx linear iterations at : 17:13:11 total time elapsed so far: 3.070000 # loops : 50 mean,max change (kT/e) : 9.6893054E-06 1.3923645E-03 energy calculations done at 3.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.250000 DelPhi exited at 17:13:11 3.256u 0.167s 0:03.87 88.1% 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 Mon Oct 10 2011 at 17:13:12 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2996 !!! WARNING: HIT 107 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.847048 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): 14.73000 72.55200 ymin,ymax (A): 3.127000 53.04500 zmin,zma (A): 6.160000 63.70200 x,y,z range (A): 57.82200 49.91800 57.54200 scale (grids/A): 1.847048 object centre (A): 43.64100 28.08600 34.93100 number of atom coordinates read : 2996 total number of charged atoms : 2854 net assigned charge : -4.485965 assigned positive charge : 453.6037 centred at (gu) : 87.05779 91.75951 94.86523 assigned negative charge : -458.0911 centred at (gu) : 86.93410 92.02583 95.19582 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 82294 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28312 grid for indexing accessible points = 1.400000 m= 28598 mr = 55112 m= 4151 mr = 20356 m= 207 mr = 2393 m= 2 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 878 time to turn everything in is 0.5800000 number of dielectric boundary points 37322 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 178 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 22370 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) : 0.6156826 object centre at (A) : 43.64100 28.08600 34.93100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8225074E-03 -5.2887290E-03 midg,1,midg; midg,igrid,midg 5.8952142E-03 -2.2490308E-02 1,midg,midg; igrid,midg,midg -5.6125835E-02 9.7296415E-03 gauss-seidel spectral radius is 0.9985976 estimated iterations to convergence 212 setup time was (sec) 0.8700000 now iterating at: 17:13:13 rms-change max change #iterations 4.380744 174.1074 at 10iterations 2.020205 65.12702 at 20iterations 0.9317421 34.64658 at 30iterations 0.4313303 13.89629 at 40iterations 0.1993210 6.839020 at 50iterations 9.2237636E-02 2.838555 at 60iterations 4.2752057E-02 1.352066 at 70iterations 1.9763868E-02 0.6627588 at 80iterations 9.1718705E-03 0.2789612 at 90iterations 4.2362530E-03 0.1265726 at 100iterations 1.9627321E-03 5.8103561E-02 at 110iterations 9.1228407E-04 3.4189224E-02 at 120iterations finished qdiffx linear iterations at : 17:13:19 total time elapsed so far: 7.510000 # loops : 120 mean,max change (kT/e) : 9.1228407E-04 3.4189224E-02 energy calculations done at 7.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.670000 DelPhi exited at 17:13:20 7.676u 0.214s 0:08.30 94.9% 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 17:13:20 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: 315 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2996 !!! WARNING: HIT 107 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.770572 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): 14.73000 72.55200 ymin,ymax (A): 3.127000 53.04500 zmin,zma (A): 6.160000 63.70200 x,y,z range (A): 57.82200 49.91800 57.54200 scale (grids/A): 2.770572 object centre (A): 43.64100 28.08600 34.93100 number of atom coordinates read : 2996 total number of charged atoms : 2854 net assigned charge : -4.485965 assigned positive charge : 453.6037 centred at (gu) : 85.58655 92.63895 97.29735 assigned negative charge : -458.0911 centred at (gu) : 85.40108 93.03851 97.79377 start vw surface at 0.1500000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 190061 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28312 grid for indexing accessible points = 1.400000 m= 93107 mr = 133913 m= 32326 mr = 74588 m= 7263 mr = 25302 m= 848 mr = 5205 m= 48 mr = 505 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 3129 time to turn everything in is 1.430000 number of dielectric boundary points 84134 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.550000 number of grid points assigned charge 22828 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) : 1.847048 object centre at (A) : 43.64100 28.08600 34.93100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.2963487E-02 0.1910986 midg,1,midg; midg,igrid,midg 7.5228482E-02 -0.2162672 1,midg,midg; igrid,midg,midg -0.7418521 0.1770796 gauss-seidel spectral radius is 0.9992736 estimated iterations to convergence 293 setup time was (sec) 1.720000 now iterating at: 17:13:22 rms-change max change #iterations 10.65517 415.3719 at 10iterations 6.335453 140.4619 at 20iterations 3.736438 83.27475 at 30iterations 2.186611 47.40831 at 40iterations 1.274930 31.77812 at 50iterations 0.7430635 13.94429 at 60iterations 0.4320275 8.817734 at 70iterations 0.2509308 4.937112 at 80iterations 0.1455248 2.693016 at 90iterations 8.4171094E-02 1.650933 at 100iterations 4.8735004E-02 0.8901157 at 110iterations 2.8184924E-02 0.6024778 at 120iterations 1.6299115E-02 0.3112402 at 130iterations 9.4163222E-03 0.1509705 at 140iterations 5.4330826E-03 9.8487854E-02 at 150iterations 3.1434575E-03 5.6444168E-02 at 160iterations 1.8132292E-03 3.1999588E-02 at 170iterations 1.0491015E-03 1.7230988E-02 at 180iterations finished qdiffx linear iterations at : 17:13:33 total time elapsed so far: 12.49000 # loops : 180 mean,max change (kT/e) : 1.0491015E-03 1.7230988E-02 energy calculations done at 12.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.66000 DelPhi exited at 17:13:33 12.667u 0.226s 0:13.37 96.3% 0+0k 0+0io 0pf+0w