Tue Oct 11 08:33:19 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 Tue Oct 11 2011 at 08:33:19 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2065 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7158513 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): 0.3050001 40.19200 ymin,ymax (A): -25.17300 18.15700 zmin,zma (A): -17.74400 31.98700 x,y,z range (A): 39.88700 43.33000 49.73100 scale (grids/A): 0.7158513 object centre (A): 20.24850 -3.508000 7.121500 number of atom coordinates read : 2065 total number of charged atoms : 1931 net assigned charge : 6.931010 assigned positive charge : 312.7771 centred at (gu) : 88.75425 90.02177 91.27939 assigned negative charge : -305.8461 centred at (gu) : 88.67911 90.18414 91.29467 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6828 nv = 96 ne = 84 npr = 43234 no. pairs analyzed = 43234 no. exposed pairs = 2326 no. arc points = 16000 no. surface atoms = 793 nbur = 1272 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 428 mr = 3970 m= 1 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 106 time to turn everything in is 0.1700000 number of dielectric boundary points 3220 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1474 ## 144 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7796 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.3635248E-08 7.9807926E-08 midg,1,midg; midg,igrid,midg 1.6407802E-07 -2.4249248E-08 1,midg,midg; igrid,midg,midg 3.4276738E-08 9.1060315E-08 gauss-seidel spectral radius is 0.9898167 estimated iterations to convergence 81 setup time was (sec) 0.3600000 now iterating at: 08:33:19 rms-change max change #iterations 0.2149486 31.68281 at 10iterations 2.7152294E-02 3.537708 at 20iterations 3.4164630E-03 0.4735389 at 30iterations 4.3619412E-04 6.0018539E-02 at 40iterations 5.4815748E-05 7.3423386E-03 at 50iterations finished qdiffx linear iterations at : 08:33:22 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 5.4815748E-05 7.3423386E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 08:33:23 3.307u 0.169s 0:04.17 82.9% 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 Tue Oct 11 2011 at 08:33:23 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2065 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.147554 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): 0.3050001 40.19200 ymin,ymax (A): -25.17300 18.15700 zmin,zma (A): -17.74400 31.98700 x,y,z range (A): 39.88700 43.33000 49.73100 scale (grids/A): 2.147554 object centre (A): 20.24850 -3.508000 7.121500 number of atom coordinates read : 2065 total number of charged atoms : 1931 net assigned charge : 6.931010 assigned positive charge : 312.7771 centred at (gu) : 86.26282 90.06528 93.83820 assigned negative charge : -305.8461 centred at (gu) : 86.03737 90.55250 93.88398 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 73123 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16000 grid for indexing accessible points = 1.400000 m= 27622 mr = 52440 m= 5138 mr = 20735 m= 605 mr = 3408 m= 20 mr = 354 m= 0 mr = 4 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 3014 time to turn everything in is 0.3600000 number of dielectric boundary points 29567 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 76 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 15363 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) : 0.7158513 object centre at (A) : 20.24850 -3.508000 7.121500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1169980E-02 5.6781255E-02 midg,1,midg; midg,igrid,midg 5.1376823E-02 5.0263358E-03 1,midg,midg; igrid,midg,midg 2.6774175E-02 1.3624952E-02 gauss-seidel spectral radius is 0.9988444 estimated iterations to convergence 233 setup time was (sec) 0.5800000 now iterating at: 08:33:24 rms-change max change #iterations 4.654956 204.9759 at 10iterations 2.317817 78.33363 at 20iterations 1.150588 35.92207 at 30iterations 0.5741389 17.30446 at 40iterations 0.2868234 9.453864 at 50iterations 0.1424245 4.725197 at 60iterations 7.1115717E-02 2.324163 at 70iterations 3.5538122E-02 1.044950 at 80iterations 1.7638054E-02 0.5439911 at 90iterations 8.8225743E-03 0.2910080 at 100iterations 4.4055521E-03 0.1388779 at 110iterations 2.2018799E-03 7.0193291E-02 at 120iterations finished qdiffx linear iterations at : 08:33:31 total time elapsed so far: 7.530000 # loops : 120 mean,max change (kT/e) : 2.2018799E-03 7.0193291E-02 energy calculations done at 7.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.670000 DelPhi exited at 08:33:31 7.668u 0.190s 0:08.16 96.2% 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 Tue Oct 11 2011 at 08:33:31 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: 274 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2065 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.221331 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): 0.3050001 40.19200 ymin,ymax (A): -25.17300 18.15700 zmin,zma (A): -17.74400 31.98700 x,y,z range (A): 39.88700 43.33000 49.73100 scale (grids/A): 3.221331 object centre (A): 20.24850 -3.508000 7.121500 number of atom coordinates read : 2065 total number of charged atoms : 1931 net assigned charge : 6.931010 assigned positive charge : 312.7771 centred at (gu) : 84.39433 90.09800 95.75741 assigned negative charge : -305.8461 centred at (gu) : 84.05608 90.82883 95.82615 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 168929 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16000 grid for indexing accessible points = 1.400000 m= 87802 mr = 126118 m= 33812 mr = 73054 m= 9698 mr = 27659 m= 2208 mr = 7468 m= 319 mr = 1665 m= 20 mr = 239 m= 0 mr = 3 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 10223 time to turn everything in is 1.110000 number of dielectric boundary points 66582 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 15448 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) : 2.147554 object centre at (A) : 20.24850 -3.508000 7.121500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3505780 0.4523436 midg,1,midg; midg,igrid,midg 0.3738236 5.7367641E-02 1,midg,midg; igrid,midg,midg 0.3127558 7.1375541E-02 gauss-seidel spectral radius is 0.9992945 estimated iterations to convergence 297 setup time was (sec) 1.340000 now iterating at: 08:33:33 rms-change max change #iterations 10.30825 388.3758 at 10iterations 6.099031 156.3422 at 20iterations 3.598112 85.87686 at 30iterations 2.124224 43.24990 at 40iterations 1.247600 23.98359 at 50iterations 0.7344124 14.42059 at 60iterations 0.4297529 7.931380 at 70iterations 0.2511721 4.429773 at 80iterations 0.1474852 2.860079 at 90iterations 8.6388811E-02 1.706345 at 100iterations 5.0611772E-02 0.9297409 at 110iterations 2.9640526E-02 0.5672607 at 120iterations 1.7446503E-02 0.3160038 at 130iterations 1.0300262E-02 0.1803160 at 140iterations 6.1181700E-03 0.1056275 at 150iterations 3.6879748E-03 6.8639755E-02 at 160iterations 2.2646820E-03 4.4441223E-02 at 170iterations 1.4347901E-03 2.6170731E-02 at 180iterations finished qdiffx linear iterations at : 08:33:44 total time elapsed so far: 12.44000 # loops : 180 mean,max change (kT/e) : 1.4347901E-03 2.6170731E-02 energy calculations done at 12.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.57000 DelPhi exited at 08:33:45 12.572u 0.204s 0:13.26 96.3% 0+0k 0+0io 0pf+0w