Mon Oct 10 19:32:28 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 Mon Oct 10 2011 at 19:32:28 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2645 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: 0.6709512 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): -20.05600 31.59700 ymin,ymax (A): -7.008000 46.05100 zmin,zma (A): 34.68200 87.04601 x,y,z range (A): 51.65300 53.05900 52.36401 scale (grids/A): 0.6709512 object centre (A): 5.770500 19.52150 60.86400 number of atom coordinates read : 2645 total number of charged atoms : 2507 net assigned charge : 2.000008 assigned positive charge : 398.1934 centred at (gu) : 90.45326 90.42912 89.42216 assigned negative charge : -396.1942 centred at (gu) : 90.59003 90.36856 89.40443 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8264 nv = 96 ne = 84 npr = 52675 no. pairs analyzed = 52675 no. exposed pairs = 3379 no. arc points = 23605 no. surface atoms = 1123 nbur = 1522 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 544 mr = 4653 m= 5 mr = 91 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 0.3100000 number of dielectric boundary points 4069 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2257 ## 229 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9417 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4821931E-09 1.0396332E-08 midg,1,midg; midg,igrid,midg -8.4201313E-09 2.5112683E-08 1,midg,midg; igrid,midg,midg 3.9017458E-08 -3.2981774E-08 gauss-seidel spectral radius is 0.9884935 estimated iterations to convergence 76 setup time was (sec) 0.5200000 now iterating at: 19:32:29 rms-change max change #iterations 0.1806795 23.37665 at 10iterations 2.0037854E-02 3.012226 at 20iterations 2.4567784E-03 0.3761234 at 30iterations 4.9775763E-04 7.5789452E-02 at 40iterations 1.7944782E-04 2.8352737E-02 at 50iterations finished qdiffx linear iterations at : 19:32:31 total time elapsed so far: 3.030000 # loops : 50 mean,max change (kT/e) : 1.7944782E-04 2.8352737E-02 energy calculations done at 3.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.200000 DelPhi exited at 19:32:32 3.200u 0.160s 0:04.02 83.5% 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 19:32:32 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 = 2645 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: 2.012854 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): -20.05600 31.59700 ymin,ymax (A): -7.008000 46.05100 zmin,zma (A): 34.68200 87.04601 x,y,z range (A): 51.65300 53.05900 52.36401 scale (grids/A): 2.012854 object centre (A): 5.770500 19.52150 60.86400 number of atom coordinates read : 2645 total number of charged atoms : 2507 net assigned charge : 2.000008 assigned positive charge : 398.1934 centred at (gu) : 91.35899 91.28680 88.26575 assigned negative charge : -396.1942 centred at (gu) : 91.76984 91.10538 88.21284 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 87597 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23605 grid for indexing accessible points = 1.400000 m= 35459 mr = 61283 m= 6890 mr = 27040 m= 571 mr = 4634 m= 12 mr = 262 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 1498 time to turn everything in is 0.6200000 number of dielectric boundary points 37310 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 19835 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) : 0.6709512 object centre at (A) : 5.770500 19.52150 60.86400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1132151E-02 -1.3841978E-02 midg,1,midg; midg,igrid,midg -2.8985650E-03 3.8783632E-02 1,midg,midg; igrid,midg,midg 3.0633879E-03 -5.4318202E-03 gauss-seidel spectral radius is 0.9987795 estimated iterations to convergence 227 setup time was (sec) 0.9000000 now iterating at: 19:32:33 rms-change max change #iterations 4.786237 209.3993 at 10iterations 2.329181 89.51706 at 20iterations 1.135897 31.61920 at 30iterations 0.5571517 16.59916 at 40iterations 0.2715408 7.665955 at 50iterations 0.1325932 3.537439 at 60iterations 6.5067507E-02 1.861702 at 70iterations 3.1745974E-02 0.8673439 at 80iterations 1.5597096E-02 0.4579582 at 90iterations 7.7303927E-03 0.2195244 at 100iterations 3.8986835E-03 0.1151276 at 110iterations 2.0291181E-03 5.6441307E-02 at 120iterations finished qdiffx linear iterations at : 19:32:40 total time elapsed so far: 7.350000 # loops : 120 mean,max change (kT/e) : 2.0291181E-03 5.6441307E-02 energy calculations done at 7.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.530000 DelPhi exited at 19:32:41 7.532u 0.202s 0:08.65 89.3% 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 Mon Oct 10 2011 at 19:32:41 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 = 2645 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.019280 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): -20.05600 31.59700 ymin,ymax (A): -7.008000 46.05100 zmin,zma (A): 34.68200 87.04601 x,y,z range (A): 51.65300 53.05900 52.36401 scale (grids/A): 3.019280 object centre (A): 5.770500 19.52150 60.86400 number of atom coordinates read : 2645 total number of charged atoms : 2507 net assigned charge : 2.000008 assigned positive charge : 398.1934 centred at (gu) : 92.03832 91.93000 87.39850 assigned negative charge : -396.1942 centred at (gu) : 92.65475 91.65802 87.31934 start vw surface at 0.1500000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 201446 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23605 grid for indexing accessible points = 1.400000 m= 109788 mr = 147565 m= 45635 mr = 91246 m= 12920 mr = 37671 m= 2460 mr = 10098 m= 211 mr = 1775 m= 2 mr = 127 m= 0 mr = 0 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 5217 time to turn everything in is 1.620000 number of dielectric boundary points 83980 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.750000 number of grid points assigned charge 20056 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) : 2.012854 object centre at (A) : 5.770500 19.52150 60.86400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2436599 3.7008960E-02 midg,1,midg; midg,igrid,midg -0.1385775 0.4291249 1,midg,midg; igrid,midg,midg -0.1983022 0.1980495 gauss-seidel spectral radius is 0.9992958 estimated iterations to convergence 297 setup time was (sec) 1.930000 now iterating at: 19:32:43 rms-change max change #iterations 10.99261 410.7397 at 10iterations 6.513318 127.5539 at 20iterations 3.852930 84.24066 at 30iterations 2.270680 41.12429 at 40iterations 1.337204 22.89817 at 50iterations 0.7846430 13.62983 at 60iterations 0.4605882 8.239326 at 70iterations 0.2694753 4.631729 at 80iterations 0.1573394 2.872640 at 90iterations 9.2271380E-02 1.691070 at 100iterations 5.3931855E-02 0.9307594 at 110iterations 3.1496722E-02 0.5127059 at 120iterations 1.8392893E-02 0.2872772 at 130iterations 1.0743625E-02 0.1811466 at 140iterations 6.2986030E-03 0.1079221 at 150iterations 3.6903084E-03 6.2788010E-02 at 160iterations 2.1789640E-03 3.9279938E-02 at 170iterations 1.2975067E-03 2.0990372E-02 at 180iterations finished qdiffx linear iterations at : 19:32:54 total time elapsed so far: 12.68000 # loops : 180 mean,max change (kT/e) : 1.2975067E-03 2.0990372E-02 energy calculations done at 12.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.86000 DelPhi exited at 19:32:55 12.859u 0.235s 0:13.62 96.0% 0+0k 0+0io 0pf+0w