Tue Oct 11 07:55:56 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 07:55:56 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2312 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 0.7190467 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): 3.884000 53.39400 ymin,ymax (A): -7.775000 39.53700 zmin,zma (A): -24.26500 19.96600 x,y,z range (A): 49.51000 47.31200 44.23100 scale (grids/A): 0.7190467 object centre (A): 28.63900 15.88100 -2.149500 number of atom coordinates read : 2312 total number of charged atoms : 2174 net assigned charge : 3.525008 assigned positive charge : 344.9345 centred at (gu) : 91.08247 90.50623 90.65626 assigned negative charge : -341.4099 centred at (gu) : 91.15283 90.30669 90.56086 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8148 nv = 96 ne = 84 npr = 47208 no. pairs analyzed = 47208 no. exposed pairs = 2750 no. arc points = 19701 no. surface atoms = 927 nbur = 1385 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 551 mr = 4734 m= 4 mr = 100 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3869 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1784 ## 186 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 8958 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4976584E-08 1.1841089E-07 midg,1,midg; midg,igrid,midg -9.3440541E-08 1.9294417E-07 1,midg,midg; igrid,midg,midg 7.0920002E-08 -1.4235362E-08 gauss-seidel spectral radius is 0.9899409 estimated iterations to convergence 81 setup time was (sec) 0.5100000 now iterating at: 07:55:57 rms-change max change #iterations 0.2292590 27.97950 at 10iterations 2.9380845E-02 4.355728 at 20iterations 3.7431815E-03 0.4498234 at 30iterations 4.7527332E-04 6.4532757E-02 at 40iterations 6.1214247E-05 6.9770813E-03 at 50iterations finished qdiffx linear iterations at : 07:55:59 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 6.1214247E-05 6.9770813E-03 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 07:56:00 3.090u 0.147s 0:03.52 91.7% 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 07:56:00 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2312 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 2.157140 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): 3.884000 53.39400 ymin,ymax (A): -7.775000 39.53700 zmin,zma (A): -24.26500 19.96600 x,y,z range (A): 49.51000 47.31200 44.23100 scale (grids/A): 2.157140 object centre (A): 28.63900 15.88100 -2.149500 number of atom coordinates read : 2312 total number of charged atoms : 2174 net assigned charge : 3.525008 assigned positive charge : 344.9345 centred at (gu) : 93.24718 91.51820 91.96864 assigned negative charge : -341.4099 centred at (gu) : 93.45837 90.91994 91.68253 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 86384 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19701 grid for indexing accessible points = 1.400000 m= 34467 mr = 61255 m= 6913 mr = 26560 m= 624 mr = 4817 m= 17 mr = 315 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 35458 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 61 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 17289 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) : 0.7190467 object centre at (A) : 28.63900 15.88100 -2.149500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4652667E-02 3.9865211E-02 midg,1,midg; midg,igrid,midg 3.1528980E-03 9.4545193E-02 1,midg,midg; igrid,midg,midg 1.9903922E-02 -8.7902155E-03 gauss-seidel spectral radius is 0.9988900 estimated iterations to convergence 238 setup time was (sec) 0.8500000 now iterating at: 07:56:01 rms-change max change #iterations 5.045423 201.9650 at 10iterations 2.539745 86.59795 at 20iterations 1.285606 40.06036 at 30iterations 0.6495436 17.85513 at 40iterations 0.3284284 10.22299 at 50iterations 0.1663714 4.410186 at 60iterations 8.3792433E-02 2.409029 at 70iterations 4.2467169E-02 1.133026 at 80iterations 2.1415772E-02 0.5916033 at 90iterations 1.0844043E-02 0.3099365 at 100iterations 5.4718675E-03 0.1543794 at 110iterations 2.7641330E-03 7.7497959E-02 at 120iterations finished qdiffx linear iterations at : 07:56:07 total time elapsed so far: 6.770000 # loops : 120 mean,max change (kT/e) : 2.7641330E-03 7.7497959E-02 energy calculations done at 6.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.950000 DelPhi exited at 07:56:08 6.954u 0.161s 0:08.04 88.4% 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 07:56:08 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: 253 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2312 !!! WARNING: SEP 190 has a net charge of -0.4750 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: 3.235710 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): 3.884000 53.39400 ymin,ymax (A): -7.775000 39.53700 zmin,zma (A): -24.26500 19.96600 x,y,z range (A): 49.51000 47.31200 44.23100 scale (grids/A): 3.235710 object centre (A): 28.63900 15.88100 -2.149500 number of atom coordinates read : 2312 total number of charged atoms : 2174 net assigned charge : 3.525008 assigned positive charge : 344.9345 centred at (gu) : 94.87066 92.27743 92.95291 assigned negative charge : -341.4099 centred at (gu) : 95.18753 91.37983 92.52376 start vw surface at 0.1300000 fill in re-entrant regions at 0.8700000 boundary points on vw surface= 199232 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19701 grid for indexing accessible points = 1.400000 m= 107112 mr = 147383 m= 44362 mr = 89790 m= 13276 mr = 36941 m= 2704 mr = 10550 m= 271 mr = 2088 m= 16 mr = 181 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.9400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.920000 number of dielectric boundary points 80037 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.040000 number of grid points assigned charge 17384 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) : 2.157140 object centre at (A) : 28.63900 15.88100 -2.149500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3314210 0.3343271 midg,1,midg; midg,igrid,midg 4.5547493E-02 0.8545894 1,midg,midg; igrid,midg,midg 8.0754802E-02 -7.1216114E-03 gauss-seidel spectral radius is 0.9993110 estimated iterations to convergence 301 setup time was (sec) 2.190000 now iterating at: 07:56:10 rms-change max change #iterations 10.89879 381.8629 at 10iterations 6.419042 119.1532 at 20iterations 3.779352 63.52785 at 30iterations 2.225783 37.93051 at 40iterations 1.305389 22.54034 at 50iterations 0.7657288 12.41444 at 60iterations 0.4491200 7.524872 at 70iterations 0.2633386 4.026465 at 80iterations 0.1547107 2.514759 at 90iterations 9.0679899E-02 1.457565 at 100iterations 5.3272411E-02 0.8253517 at 110iterations 3.1293988E-02 0.5030518 at 120iterations 1.8412530E-02 0.3546104 at 130iterations 1.0851891E-02 0.1759949 at 140iterations 6.4460440E-03 9.9017859E-02 at 150iterations 3.8304145E-03 6.2503815E-02 at 160iterations 2.3058988E-03 3.7605286E-02 at 170iterations 1.4057325E-03 2.3979187E-02 at 180iterations finished qdiffx linear iterations at : 07:56:20 total time elapsed so far: 11.71000 # loops : 180 mean,max change (kT/e) : 1.4057325E-03 2.3979187E-02 energy calculations done at 11.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.88000 DelPhi exited at 07:56:20 11.879u 0.184s 0:12.35 97.5% 0+0k 0+0io 0pf+0w