Sun Oct 9 07:50:23 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 07:50:23 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2211 !!! WARNING: NAP 207 has a net charge of -2.0000 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: 0.7096581 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): -15.84000 30.74000 ymin,ymax (A): -19.92300 30.24200 zmin,zma (A): -5.093000 35.55600 x,y,z range (A): 46.58000 50.16500 40.64900 scale (grids/A): 0.7096581 object centre (A): 7.450000 5.159499 15.23150 number of atom coordinates read : 2211 total number of charged atoms : 2074 net assigned charge : 6.000018 assigned positive charge : 332.2636 centred at (gu) : 89.77198 90.65733 90.66906 assigned negative charge : -326.2639 centred at (gu) : 89.64984 90.75900 90.80183 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7485 nv = 96 ne = 84 npr = 45988 no. pairs analyzed = 45988 no. exposed pairs = 2698 no. arc points = 19108 no. surface atoms = 912 nbur = 1299 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 489 mr = 4230 m= 1 mr = 103 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 193 time to turn everything in is 0.3300000 number of dielectric boundary points 3642 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1813 ## 177 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8418 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1042771E-07 -2.1612529E-08 midg,1,midg; midg,igrid,midg 9.6197709E-08 -1.8393280E-09 1,midg,midg; igrid,midg,midg -1.3287295E-08 1.1485984E-07 gauss-seidel spectral radius is 0.9896647 estimated iterations to convergence 80 setup time was (sec) 0.6000000 now iterating at: 07:50:24 rms-change max change #iterations 0.2126427 29.83165 at 10iterations 2.6153779E-02 3.387154 at 20iterations 3.2401260E-03 0.3976860 at 30iterations 4.0777546E-04 6.3192368E-02 at 40iterations 4.8986152E-05 6.0796738E-03 at 50iterations finished qdiffx linear iterations at : 07:50:27 total time elapsed so far: 3.870000 # loops : 50 mean,max change (kT/e) : 4.8986152E-05 6.0796738E-03 energy calculations done at 3.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.050000 DelPhi exited at 07:50:28 4.049u 0.252s 0:04.57 93.8% 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 07:50:28 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2211 !!! WARNING: NAP 207 has a net charge of -2.0000 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: 2.128974 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): -15.84000 30.74000 ymin,ymax (A): -19.92300 30.24200 zmin,zma (A): -5.093000 35.55600 x,y,z range (A): 46.58000 50.16500 40.64900 scale (grids/A): 2.128974 object centre (A): 7.450000 5.159499 15.23150 number of atom coordinates read : 2211 total number of charged atoms : 2074 net assigned charge : 6.000018 assigned positive charge : 332.2636 centred at (gu) : 89.31541 91.97192 92.00688 assigned negative charge : -326.2639 centred at (gu) : 88.94952 92.27702 92.40542 start vw surface at 0.1500000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 78281 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19108 grid for indexing accessible points = 1.400000 m= 31896 mr = 54078 m= 6695 mr = 24717 m= 679 mr = 4713 m= 27 mr = 379 m= 0 mr = 13 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 4656 time to turn everything in is 0.7300000 number of dielectric boundary points 33678 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 85 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 16484 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) : 0.7096581 object centre at (A) : 7.450000 5.159499 15.23150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9000766E-02 2.1465642E-02 midg,1,midg; midg,igrid,midg 5.0660208E-02 6.7103698E-05 1,midg,midg; igrid,midg,midg -1.8155636E-02 3.2873351E-02 gauss-seidel spectral radius is 0.9988521 estimated iterations to convergence 234 setup time was (sec) 1.030000 now iterating at: 07:50:29 rms-change max change #iterations 4.829551 201.8101 at 10iterations 2.398858 80.28748 at 20iterations 1.193167 36.62506 at 30iterations 0.5961034 17.78456 at 40iterations 0.2967161 9.675865 at 50iterations 0.1478478 5.581753 at 60iterations 7.3974445E-02 2.067980 at 70iterations 3.6879003E-02 1.171263 at 80iterations 1.8375373E-02 0.5596194 at 90iterations 9.1440883E-03 0.2527218 at 100iterations 4.5646545E-03 0.1372681 at 110iterations 2.2802816E-03 6.9288254E-02 at 120iterations finished qdiffx linear iterations at : 07:50:37 total time elapsed so far: 9.340000 # loops : 120 mean,max change (kT/e) : 2.2802816E-03 6.9288254E-02 energy calculations done at 9.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.510000 DelPhi exited at 07:50:38 9.513u 0.291s 0:10.07 97.3% 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 07:50:38 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2211 !!! WARNING: NAP 207 has a net charge of -2.0000 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: 3.193461 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): -15.84000 30.74000 ymin,ymax (A): -19.92300 30.24200 zmin,zma (A): -5.093000 35.55600 x,y,z range (A): 46.58000 50.16500 40.64900 scale (grids/A): 3.193461 object centre (A): 7.450000 5.159499 15.23150 number of atom coordinates read : 2211 total number of charged atoms : 2074 net assigned charge : 6.000018 assigned positive charge : 332.2636 centred at (gu) : 88.97308 92.95783 93.01012 assigned negative charge : -326.2639 centred at (gu) : 88.42420 93.41555 93.60812 start vw surface at 0.1400000 fill in re-entrant regions at 1.050000 boundary points on vw surface= 180032 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19108 grid for indexing accessible points = 1.400000 m= 97305 mr = 129984 m= 42491 mr = 81612 m= 12821 mr = 35584 m= 2728 mr = 10289 m= 402 mr = 2096 m= 26 mr = 313 m= 0 mr = 15 time to grow re-entrant surface = 1.160000 no. cavity mid-points inaccessible to solvent = 15877 time to turn everything in is 2.330000 number of dielectric boundary points 75912 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.480000 number of grid points assigned charge 16592 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) : 2.128974 object centre at (A) : 7.450000 5.159499 15.23150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6232223 0.1784251 midg,1,midg; midg,igrid,midg 0.4431257 0.1629412 1,midg,midg; igrid,midg,midg -0.1084688 0.2182435 gauss-seidel spectral radius is 0.9992952 estimated iterations to convergence 297 setup time was (sec) 2.650000 now iterating at: 07:50:41 rms-change max change #iterations 10.58944 440.5837 at 10iterations 6.156063 135.7846 at 20iterations 3.582144 66.71314 at 30iterations 2.087213 36.83800 at 40iterations 1.216127 20.80276 at 50iterations 0.7077199 12.67869 at 60iterations 0.4118969 7.789584 at 70iterations 0.2392784 4.084041 at 80iterations 0.1392241 2.399210 at 90iterations 8.0809966E-02 1.311429 at 100iterations 4.7003813E-02 0.8402381 at 110iterations 2.7292643E-02 0.4380240 at 120iterations 1.5900398E-02 0.2687531 at 130iterations 9.2523787E-03 0.1546555 at 140iterations 5.3755832E-03 8.5178375E-02 at 150iterations 3.1321377E-03 5.5929184E-02 at 160iterations 1.8209151E-03 3.1608582E-02 at 170iterations 1.0606610E-03 1.8423080E-02 at 180iterations finished qdiffx linear iterations at : 07:50:54 total time elapsed so far: 16.32000 # loops : 180 mean,max change (kT/e) : 1.0606610E-03 1.8423080E-02 energy calculations done at 16.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.50000 DelPhi exited at 07:50:55 16.502u 0.329s 0:17.16 98.0% 0+0k 0+0io 0pf+0w