Tue Oct 11 06:00:48 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 06:00:48 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: 349 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7086692 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): 25.68600 72.53800 ymin,ymax (A): -18.66800 31.56700 zmin,zma (A): 4.031000 46.32200 x,y,z range (A): 46.85201 50.23500 42.29100 scale (grids/A): 0.7086692 object centre (A): 49.11200 6.449500 25.17650 number of atom coordinates read : 2318 total number of charged atoms : 1988 net assigned charge : 5.945011 assigned positive charge : 325.7760 centred at (gu) : 89.06451 90.16398 90.30813 assigned negative charge : -319.8310 centred at (gu) : 89.19172 90.10036 90.39184 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7174 nv = 96 ne = 84 npr = 42905 no. pairs analyzed = 42905 no. exposed pairs = 2587 no. arc points = 17374 no. surface atoms = 887 nbur = 1431 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 464 mr = 4131 m= 3 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3423 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1650 ## 173 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8033 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.8873207E-08 7.3587705E-09 midg,1,midg; midg,igrid,midg 1.7255617E-08 8.6686860E-08 1,midg,midg; igrid,midg,midg 1.3983548E-07 -1.2830109E-08 gauss-seidel spectral radius is 0.9896216 estimated iterations to convergence 80 setup time was (sec) 0.5100000 now iterating at: 06:00:49 rms-change max change #iterations 0.2077168 34.47377 at 10iterations 2.6246959E-02 4.143032 at 20iterations 3.5803411E-03 0.4496422 at 30iterations 6.4317568E-04 9.1106415E-02 at 40iterations 1.6758921E-04 1.8724442E-02 at 50iterations finished qdiffx linear iterations at : 06:00:52 total time elapsed so far: 3.050000 # loops : 50 mean,max change (kT/e) : 1.6758921E-04 1.8724442E-02 energy calculations done at 3.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.240000 DelPhi exited at 06:00:52 3.242u 0.176s 0:04.06 83.9% 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 06:00:53 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: 349 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.126008 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): 25.68600 72.53800 ymin,ymax (A): -18.66800 31.56700 zmin,zma (A): 4.031000 46.32200 x,y,z range (A): 46.85201 50.23500 42.29100 scale (grids/A): 2.126008 object centre (A): 49.11200 6.449500 25.17650 number of atom coordinates read : 2318 total number of charged atoms : 1988 net assigned charge : 5.945011 assigned positive charge : 325.7760 centred at (gu) : 87.19338 90.49207 90.92426 assigned negative charge : -319.8310 centred at (gu) : 87.57525 90.30111 91.17567 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 76026 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17374 grid for indexing accessible points = 1.400000 m= 30945 mr = 54268 m= 6076 mr = 23665 m= 584 mr = 4080 m= 22 mr = 295 m= 0 mr = 4 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 31341 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 62 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 15772 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) : 0.7086692 object centre at (A) : 49.11200 6.449500 25.17650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1552781E-02 2.8112778E-02 midg,1,midg; midg,igrid,midg 3.9623883E-02 2.9892851E-02 1,midg,midg; igrid,midg,midg 4.3890994E-02 -4.3819506E-02 gauss-seidel spectral radius is 0.9988362 estimated iterations to convergence 232 setup time was (sec) 0.8600000 now iterating at: 06:00:54 rms-change max change #iterations 4.691589 183.6304 at 10iterations 2.322855 75.07793 at 20iterations 1.153319 39.82180 at 30iterations 0.5739715 16.64661 at 40iterations 0.2865421 8.766827 at 50iterations 0.1421970 4.162462 at 60iterations 7.0686691E-02 1.955613 at 70iterations 3.5378601E-02 1.146297 at 80iterations 1.7652126E-02 0.5308304 at 90iterations 8.9011611E-03 0.2823792 at 100iterations 4.5048110E-03 0.1407270 at 110iterations 2.3468707E-03 6.8019867E-02 at 120iterations finished qdiffx linear iterations at : 06:01:00 total time elapsed so far: 7.260000 # loops : 120 mean,max change (kT/e) : 2.3468707E-03 6.8019867E-02 energy calculations done at 7.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.430000 DelPhi exited at 06:01:01 7.437u 0.212s 0:08.07 94.6% 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 06:01:01 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: 349 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2318 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 3.189012 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): 25.68600 72.53800 ymin,ymax (A): -18.66800 31.56700 zmin,zma (A): 4.031000 46.32200 x,y,z range (A): 46.85201 50.23500 42.29100 scale (grids/A): 3.189012 object centre (A): 49.11200 6.449500 25.17650 number of atom coordinates read : 2318 total number of charged atoms : 1988 net assigned charge : 5.945011 assigned positive charge : 325.7760 centred at (gu) : 85.79027 90.73817 91.38635 assigned negative charge : -319.8310 centred at (gu) : 86.36288 90.45162 91.76344 start vw surface at 0.1400000 fill in re-entrant regions at 0.8000000 boundary points on vw surface= 175181 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17374 grid for indexing accessible points = 1.400000 m= 96115 mr = 130411 m= 39334 mr = 80199 m= 11442 mr = 32510 m= 2380 mr = 8926 m= 288 mr = 1725 m= 24 mr = 200 m= 0 mr = 8 time to grow re-entrant surface = 0.8700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.790000 number of dielectric boundary points 70785 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.920000 number of grid points assigned charge 15904 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) : 2.126008 object centre at (A) : 49.11200 6.449500 25.17650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1337837 0.2414943 midg,1,midg; midg,igrid,midg 0.3089957 0.1463470 1,midg,midg; igrid,midg,midg 0.4454389 -0.5302751 gauss-seidel spectral radius is 0.9992971 estimated iterations to convergence 298 setup time was (sec) 2.090000 now iterating at: 06:01:03 rms-change max change #iterations 10.47539 295.9413 at 10iterations 6.188742 125.4644 at 20iterations 3.657887 91.87566 at 30iterations 2.156465 42.78186 at 40iterations 1.266095 24.74575 at 50iterations 0.7462387 13.75887 at 60iterations 0.4377196 7.781737 at 70iterations 0.2568933 4.946507 at 80iterations 0.1506055 2.563114 at 90iterations 8.8389806E-02 1.572218 at 100iterations 5.2026734E-02 1.005421 at 110iterations 3.0771561E-02 0.5869465 at 120iterations 1.8345172E-02 0.3585161 at 130iterations 1.1154027E-02 0.2075577 at 140iterations 6.9635976E-03 0.1353645 at 150iterations 4.5324229E-03 9.3017578E-02 at 160iterations 3.1167890E-03 6.3499451E-02 at 170iterations 2.2589448E-03 4.6058655E-02 at 180iterations finished qdiffx linear iterations at : 06:01:13 total time elapsed so far: 12.37000 # loops : 180 mean,max change (kT/e) : 2.2589448E-03 4.6058655E-02 energy calculations done at 12.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.55000 DelPhi exited at 06:01:14 12.550u 0.238s 0:13.20 96.8% 0+0k 0+0io 0pf+0w