Sun Oct 9 22:30:51 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 Sun Oct 9 2011 at 22:30:51 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 = 3038 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: 0.6704331 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): 45.63300 98.73300 ymin,ymax (A): 2.832000 54.66000 zmin,zma (A): 15.01000 67.72900 x,y,z range (A): 53.10000 51.82800 52.71900 scale (grids/A): 0.6704331 object centre (A): 72.18300 28.74600 41.36950 number of atom coordinates read : 3038 total number of charged atoms : 2990 net assigned charge : 2.500014 assigned positive charge : 473.7188 centred at (gu) : 90.54035 89.04712 90.58433 assigned negative charge : -471.2201 centred at (gu) : 90.37157 88.93524 90.61005 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 9599 nv = 96 ne = 84 npr = 56558 no. pairs analyzed = 56558 no. exposed pairs = 4246 no. arc points = 30669 no. surface atoms = 1407 nbur = 1631 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 604 mr = 4973 m= 3 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.3200000 number of dielectric boundary points 5156 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2977 ## 268 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 11372 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4713444E-08 5.0661009E-10 midg,1,midg; midg,igrid,midg -3.2858168E-08 3.5402124E-08 1,midg,midg; igrid,midg,midg -4.0212075E-08 6.7513582E-08 gauss-seidel spectral radius is 0.9885248 estimated iterations to convergence 76 setup time was (sec) 0.5400000 now iterating at: 22:30:52 rms-change max change #iterations 0.1941021 25.30025 at 10iterations 2.1440322E-02 2.878357 at 20iterations 2.3823730E-03 0.2914448 at 30iterations 2.6582225E-04 3.5505295E-02 at 40iterations 3.6838504E-05 4.5824051E-03 at 50iterations finished qdiffx linear iterations at : 22:30:54 total time elapsed so far: 2.980000 # loops : 50 mean,max change (kT/e) : 3.6838504E-05 4.5824051E-03 energy calculations done at 2.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.160000 DelPhi exited at 22:30:55 3.160u 0.130s 0:03.63 90.6% 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 Sun Oct 9 2011 at 22:30:55 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 = 3038 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: 2.011299 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): 45.63300 98.73300 ymin,ymax (A): 2.832000 54.66000 zmin,zma (A): 15.01000 67.72900 x,y,z range (A): 53.10000 51.82800 52.71900 scale (grids/A): 2.011299 object centre (A): 72.18300 28.74600 41.36950 number of atom coordinates read : 3038 total number of charged atoms : 2990 net assigned charge : 2.500014 assigned positive charge : 473.7188 centred at (gu) : 91.62031 87.14042 91.75234 assigned negative charge : -471.2201 centred at (gu) : 91.11436 86.80547 91.83003 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 102464 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30669 grid for indexing accessible points = 1.400000 m= 38247 mr = 68914 m= 7018 mr = 27435 m= 558 mr = 4346 m= 11 mr = 221 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 1875 time to turn everything in is 0.6700000 number of dielectric boundary points 47382 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 168 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 23671 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) : 0.6704331 object centre at (A) : 72.18300 28.74600 41.36950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.7264302E-04 -1.9510854E-02 midg,1,midg; midg,igrid,midg 3.2446086E-02 4.1634765E-02 1,midg,midg; igrid,midg,midg -6.0749175E-03 2.8277488E-02 gauss-seidel spectral radius is 0.9988348 estimated iterations to convergence 232 setup time was (sec) 0.9300000 now iterating at: 22:30:56 rms-change max change #iterations 5.242933 233.8505 at 10iterations 2.602146 75.79452 at 20iterations 1.284256 34.55977 at 30iterations 0.6356589 17.73132 at 40iterations 0.3144669 8.787244 at 50iterations 0.1559559 4.317639 at 60iterations 7.7053703E-02 2.368404 at 70iterations 3.8177960E-02 0.9874725 at 80iterations 1.8899610E-02 0.5625228 at 90iterations 9.3794269E-03 0.2618141 at 100iterations 4.6398430E-03 0.1290264 at 110iterations 2.3084590E-03 5.8668137E-02 at 120iterations finished qdiffx linear iterations at : 22:31:02 total time elapsed so far: 7.170000 # loops : 120 mean,max change (kT/e) : 2.3084590E-03 5.8668137E-02 energy calculations done at 7.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.330000 DelPhi exited at 22:31:03 7.337u 0.172s 0:07.89 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 Sun Oct 9 2011 at 22:31:03 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3038 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: 3.016949 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): 45.63300 98.73300 ymin,ymax (A): 2.832000 54.66000 zmin,zma (A): 15.01000 67.72900 x,y,z range (A): 53.10000 51.82800 52.71900 scale (grids/A): 3.016949 object centre (A): 72.18300 28.74600 41.36950 number of atom coordinates read : 3038 total number of charged atoms : 2990 net assigned charge : 2.500014 assigned positive charge : 473.7188 centred at (gu) : 92.43025 85.71036 92.62825 assigned negative charge : -471.2201 centred at (gu) : 91.67152 85.20820 92.74489 start vw surface at 0.1500000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 236437 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30669 grid for indexing accessible points = 1.400000 m= 120835 mr = 167330 m= 46513 mr = 97083 m= 12724 mr = 36727 m= 2227 mr = 9380 m= 201 mr = 1504 m= 5 mr = 119 m= 0 mr = 0 time to grow re-entrant surface = 1.100000 no. cavity mid-points inaccessible to solvent = 6295 time to turn everything in is 1.770000 number of dielectric boundary points 106799 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.900000 number of grid points assigned charge 23920 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) : 2.011299 object centre at (A) : 72.18300 28.74600 41.36950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.6798369E-02 -0.3359141 midg,1,midg; midg,igrid,midg 0.2315584 0.2363223 1,midg,midg; igrid,midg,midg 0.1849390 0.3573450 gauss-seidel spectral radius is 0.9993433 estimated iterations to convergence 308 setup time was (sec) 2.060000 now iterating at: 22:31:05 rms-change max change #iterations 12.35232 424.5186 at 10iterations 7.571924 168.8821 at 20iterations 4.617101 96.77992 at 30iterations 2.801780 66.61639 at 40iterations 1.693836 36.64403 at 50iterations 1.018365 20.18958 at 60iterations 0.6133618 11.68875 at 70iterations 0.3666194 6.994326 at 80iterations 0.2198688 3.535156 at 90iterations 0.1313817 2.264644 at 100iterations 7.8306563E-02 1.233070 at 110iterations 4.6728283E-02 0.7283354 at 120iterations 2.7863398E-02 0.4461700 at 130iterations 1.6602173E-02 0.2635841 at 140iterations 9.8852050E-03 0.1573620 at 150iterations 5.8957776E-03 0.1000433 at 160iterations 3.5033904E-03 5.5586815E-02 at 170iterations 2.0847030E-03 3.4023285E-02 at 180iterations finished qdiffx linear iterations at : 22:31:15 total time elapsed so far: 11.80000 # loops : 180 mean,max change (kT/e) : 2.0847030E-03 3.4023285E-02 energy calculations done at 11.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.97000 DelPhi exited at 22:31:15 11.970u 0.180s 0:12.63 96.1% 0+0k 0+0io 0pf+0w