Tue Oct 11 06:05:10 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 06:05:10 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2320 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7246525 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): 25.85900 72.56600 ymin,ymax (A): -18.52000 30.60700 zmin,zma (A): 4.208000 46.37400 x,y,z range (A): 46.70700 49.12700 42.16600 scale (grids/A): 0.7246525 object centre (A): 49.21250 6.043500 25.29100 number of atom coordinates read : 2320 total number of charged atoms : 1994 net assigned charge : 6.039010 assigned positive charge : 326.2859 centred at (gu) : 89.18214 90.41705 90.24981 assigned negative charge : -320.2471 centred at (gu) : 89.31886 90.34967 90.32497 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7559 nv = 96 ne = 84 npr = 42579 no. pairs analyzed = 42579 no. exposed pairs = 2576 no. arc points = 17540 no. surface atoms = 884 nbur = 1436 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 533 mr = 4392 m= 2 mr = 103 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3599 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1637 ## 152 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8246 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2400417E-07 1.9700508E-08 midg,1,midg; midg,igrid,midg 2.3226685E-08 1.3448658E-07 1,midg,midg; igrid,midg,midg 2.0404948E-07 -2.2742960E-08 gauss-seidel spectral radius is 0.9900717 estimated iterations to convergence 82 setup time was (sec) 0.3700000 now iterating at: 06:05:11 rms-change max change #iterations 0.2239578 37.45589 at 10iterations 2.9844375E-02 4.119724 at 20iterations 4.3828362E-03 0.6208954 at 30iterations 8.2352961E-04 0.1043911 at 40iterations 2.2389730E-04 2.5135040E-02 at 50iterations finished qdiffx linear iterations at : 06:05:14 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 2.2389730E-04 2.5135040E-02 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 06:05:15 3.552u 0.203s 0:04.09 91.6% 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 06:05:15 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2320 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.173957 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): 25.85900 72.56600 ymin,ymax (A): -18.52000 30.60700 zmin,zma (A): 4.208000 46.37400 x,y,z range (A): 46.70700 49.12700 42.16600 scale (grids/A): 2.173957 object centre (A): 49.21250 6.043500 25.29100 number of atom coordinates read : 2320 total number of charged atoms : 1994 net assigned charge : 6.039010 assigned positive charge : 326.2859 centred at (gu) : 87.54639 91.25094 90.74948 assigned negative charge : -320.2471 centred at (gu) : 87.95657 91.04901 90.97511 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 80111 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17540 grid for indexing accessible points = 1.400000 m= 33558 mr = 57393 m= 6860 mr = 25827 m= 664 mr = 4620 m= 22 mr = 326 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 33049 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 63 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 15854 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) : 0.7246525 object centre at (A) : 49.21250 6.043500 25.29100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1669591E-02 3.4524869E-02 midg,1,midg; midg,igrid,midg 4.3666873E-02 3.4517039E-02 1,midg,midg; igrid,midg,midg 4.9418699E-02 -6.1084047E-02 gauss-seidel spectral radius is 0.9988802 estimated iterations to convergence 236 setup time was (sec) 0.6400000 now iterating at: 06:05:15 rms-change max change #iterations 4.881127 192.9834 at 10iterations 2.456816 87.44308 at 20iterations 1.237419 37.84846 at 30iterations 0.6237488 18.79731 at 40iterations 0.3148108 9.102907 at 50iterations 0.1588605 4.595423 at 60iterations 7.9913221E-02 2.392820 at 70iterations 4.0524136E-02 1.441566 at 80iterations 2.0713979E-02 0.5845852 at 90iterations 1.0583377E-02 0.3098602 at 100iterations 5.4733618E-03 0.1848221 at 110iterations 2.8977881E-03 8.3168030E-02 at 120iterations finished qdiffx linear iterations at : 06:05:23 total time elapsed so far: 7.860000 # loops : 120 mean,max change (kT/e) : 2.8977881E-03 8.3168030E-02 energy calculations done at 7.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.000000 DelPhi exited at 06:05:23 8.002u 0.209s 0:08.53 96.1% 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 06:05:23 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2320 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.260936 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): 25.85900 72.56600 ymin,ymax (A): -18.52000 30.60700 zmin,zma (A): 4.208000 46.37400 x,y,z range (A): 46.70700 49.12700 42.16600 scale (grids/A): 3.260936 object centre (A): 49.21250 6.043500 25.29100 number of atom coordinates read : 2320 total number of charged atoms : 1994 net assigned charge : 6.039010 assigned positive charge : 326.2859 centred at (gu) : 86.31954 91.87652 91.12417 assigned negative charge : -320.2471 centred at (gu) : 86.93485 91.57353 91.46274 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 184420 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17540 grid for indexing accessible points = 1.400000 m= 102918 mr = 137652 m= 43793 mr = 86370 m= 13175 mr = 36389 m= 2745 mr = 10285 m= 333 mr = 1974 m= 19 mr = 200 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.290000 number of dielectric boundary points 74527 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 15952 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) : 2.173957 object centre at (A) : 49.21250 6.043500 25.29100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.8532498E-02 0.2577042 midg,1,midg; midg,igrid,midg 0.3424642 0.1418776 1,midg,midg; igrid,midg,midg 0.4877889 -0.7163233 gauss-seidel spectral radius is 0.9993103 estimated iterations to convergence 300 setup time was (sec) 1.550000 now iterating at: 06:05:25 rms-change max change #iterations 10.78067 303.8409 at 10iterations 6.417884 121.6781 at 20iterations 3.811996 78.69839 at 30iterations 2.264118 43.23094 at 40iterations 1.339871 24.42487 at 50iterations 0.7929440 14.69928 at 60iterations 0.4680508 8.039967 at 70iterations 0.2763205 5.676594 at 80iterations 0.1630030 2.940147 at 90iterations 9.6142262E-02 1.589317 at 100iterations 5.6829024E-02 0.9452209 at 110iterations 3.3696331E-02 0.6283264 at 120iterations 2.0263765E-02 0.3439522 at 130iterations 1.2356584E-02 0.2221712 at 140iterations 7.7949376E-03 0.1436844 at 150iterations 5.1186141E-03 9.6305847E-02 at 160iterations 3.5687999E-03 6.8801880E-02 at 170iterations 2.6384327E-03 5.0853729E-02 at 180iterations finished qdiffx linear iterations at : 06:05:37 total time elapsed so far: 13.54000 # loops : 180 mean,max change (kT/e) : 2.6384327E-03 5.0853729E-02 energy calculations done at 13.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.67000 DelPhi exited at 06:05:37 13.671u 0.240s 0:14.33 97.0% 0+0k 0+0io 0pf+0w