Tue Oct 11 03:54:51 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+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 03:54:51 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2697 !!! WARNING: HIR 79 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6614887 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): -11.39700 36.71000 ymin,ymax (A): -26.76300 21.55700 zmin,zma (A): -8.264000 45.55400 x,y,z range (A): 48.10700 48.32000 53.81800 scale (grids/A): 0.6614887 object centre (A): 12.65650 -2.603001 18.64500 number of atom coordinates read : 2697 total number of charged atoms : 2549 net assigned charge : 2.514015 assigned positive charge : 411.4369 centred at (gu) : 90.22118 90.25430 91.39430 assigned negative charge : -408.9233 centred at (gu) : 89.92641 90.07729 91.38891 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7889 nv = 96 ne = 84 npr = 55674 no. pairs analyzed = 55674 no. exposed pairs = 3176 no. arc points = 22202 no. surface atoms = 1064 nbur = 1633 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 468 mr = 4601 m= 2 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.3600000 number of dielectric boundary points 3704 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2203 ## 228 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9351 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.0577044E-09 1.0176381E-08 midg,1,midg; midg,igrid,midg -3.0777663E-08 4.6480778E-08 1,midg,midg; igrid,midg,midg -5.6539378E-08 7.1542203E-08 gauss-seidel spectral radius is 0.9881594 estimated iterations to convergence 75 setup time was (sec) 0.6300000 now iterating at: 03:54:52 rms-change max change #iterations 0.1750841 21.27921 at 10iterations 1.9143289E-02 2.324257 at 20iterations 2.0926653E-03 0.2554817 at 30iterations 2.5378331E-04 4.1606903E-02 at 40iterations 4.0166156E-05 5.3176880E-03 at 50iterations finished qdiffx linear iterations at : 03:54:55 total time elapsed so far: 3.900000 # loops : 50 mean,max change (kT/e) : 4.0166156E-05 5.3176880E-03 energy calculations done at 3.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.070000 DelPhi exited at 03:54:56 4.073u 0.263s 0:04.90 88.3% 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 Tue Oct 11 2011 at 03:54:56 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2697 !!! WARNING: HIR 79 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.984466 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): -11.39700 36.71000 ymin,ymax (A): -26.76300 21.55700 zmin,zma (A): -8.264000 45.55400 x,y,z range (A): 48.10700 48.32000 53.81800 scale (grids/A): 1.984466 object centre (A): 12.65650 -2.603001 18.64500 number of atom coordinates read : 2697 total number of charged atoms : 2549 net assigned charge : 2.514015 assigned positive charge : 411.4369 centred at (gu) : 90.66310 90.76243 94.18238 assigned negative charge : -408.9233 centred at (gu) : 89.77879 90.23160 94.16616 start vw surface at 0.1600000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 85019 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22202 grid for indexing accessible points = 1.400000 m= 32839 mr = 60920 m= 5536 mr = 24964 m= 353 mr = 3625 m= 2 mr = 151 m= 0 mr = 0 time to grow re-entrant surface = 0.3900000 no. cavity mid-points inaccessible to solvent = 984 time to turn everything in is 0.7500000 number of dielectric boundary points 34089 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 137 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 20119 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) : 0.6614887 object centre at (A) : 12.65650 -2.603001 18.64500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5912818E-02 -9.2007862E-03 midg,1,midg; midg,igrid,midg -1.7115474E-02 3.1337742E-02 1,midg,midg; igrid,midg,midg -1.5499522E-02 8.2457379E-02 gauss-seidel spectral radius is 0.9987447 estimated iterations to convergence 224 setup time was (sec) 1.030000 now iterating at: 03:54:57 rms-change max change #iterations 4.770125 224.7252 at 10iterations 2.318104 68.76699 at 20iterations 1.119842 33.26434 at 30iterations 0.5430483 17.34440 at 40iterations 0.2632374 7.646886 at 50iterations 0.1272632 3.715351 at 60iterations 6.1745685E-02 1.774539 at 70iterations 2.9886512E-02 0.8385010 at 80iterations 1.4479188E-02 0.4127426 at 90iterations 7.0242230E-03 0.1921120 at 100iterations 3.4275462E-03 0.1081314 at 110iterations 1.6719614E-03 5.2928925E-02 at 120iterations finished qdiffx linear iterations at : 03:55:06 total time elapsed so far: 9.340000 # loops : 120 mean,max change (kT/e) : 1.6719614E-03 5.2928925E-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 03:55:06 9.512u 0.315s 0:10.22 96.0% 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 Tue Oct 11 2011 at 03:55:06 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2697 !!! WARNING: HIR 79 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.976699 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): -11.39700 36.71000 ymin,ymax (A): -26.76300 21.55700 zmin,zma (A): -8.264000 45.55400 x,y,z range (A): 48.10700 48.32000 53.81800 scale (grids/A): 2.976699 object centre (A): 12.65650 -2.603001 18.64500 number of atom coordinates read : 2697 total number of charged atoms : 2549 net assigned charge : 2.514015 assigned positive charge : 411.4369 centred at (gu) : 90.99457 91.14366 96.27338 assigned negative charge : -408.9233 centred at (gu) : 89.66817 90.34745 96.24919 start vw surface at 0.1500000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 196218 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22202 grid for indexing accessible points = 1.400000 m= 104653 mr = 146435 m= 40101 mr = 87671 m= 10160 mr = 32943 m= 1498 mr = 7764 m= 100 mr = 1048 m= 4 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 1.210000 no. cavity mid-points inaccessible to solvent = 3336 time to turn everything in is 1.970000 number of dielectric boundary points 76831 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.120000 number of grid points assigned charge 20388 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) : 1.984466 object centre at (A) : 12.65650 -2.603001 18.64500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1951555 0.2042911 midg,1,midg; midg,igrid,midg -0.1875636 0.3772265 1,midg,midg; igrid,midg,midg -5.0361753E-02 0.7010138 gauss-seidel spectral radius is 0.9992834 estimated iterations to convergence 295 setup time was (sec) 2.290000 now iterating at: 03:55:09 rms-change max change #iterations 10.99943 423.9948 at 10iterations 6.479045 160.1570 at 20iterations 3.805730 73.81768 at 30iterations 2.230534 45.56562 at 40iterations 1.305958 26.08946 at 50iterations 0.7627777 15.14427 at 60iterations 0.4456595 8.392960 at 70iterations 0.2597553 4.454652 at 80iterations 0.1517606 2.650716 at 90iterations 8.8149279E-02 1.566264 at 100iterations 5.1359314E-02 0.8880463 at 110iterations 2.9917605E-02 0.5311584 at 120iterations 1.7434172E-02 0.3021545 at 130iterations 1.0161275E-02 0.1709423 at 140iterations 5.9303171E-03 9.9344492E-02 at 150iterations 3.4830326E-03 5.8411598E-02 at 160iterations 2.0555439E-03 3.5087585E-02 at 170iterations 1.2292006E-03 2.3777008E-02 at 180iterations finished qdiffx linear iterations at : 03:55:23 total time elapsed so far: 16.07000 # loops : 180 mean,max change (kT/e) : 1.2292006E-03 2.3777008E-02 energy calculations done at 16.07000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.24000 DelPhi exited at 03:55:23 16.243u 0.313s 0:17.01 97.2% 0+0k 0+0io 0pf+0w