Tue Oct 11 07:53:57 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+sph.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 = amb.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 07:53:57 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2380 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: 0.6433076 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): -1.551000 53.78800 ymin,ymax (A): -22.78400 22.90800 zmin,zma (A): 8.827000 53.88100 x,y,z range (A): 55.33900 45.69200 45.05400 scale (grids/A): 0.6433076 object centre (A): 26.11850 6.1999321E-02 31.35400 number of atom coordinates read : 2380 total number of charged atoms : 2244 net assigned charge : 5.500007 assigned positive charge : 357.6723 centred at (gu) : 88.65172 90.32522 90.07819 assigned negative charge : -352.1728 centred at (gu) : 88.66954 90.26813 89.89734 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6636 nv = 96 ne = 84 npr = 48090 no. pairs analyzed = 48090 no. exposed pairs = 2839 no. arc points = 19949 no. surface atoms = 965 nbur = 1415 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 356 mr = 3732 m= 2 mr = 42 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 0.1800000 number of dielectric boundary points 3220 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1977 ## 212 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7861 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2367843E-08 2.9728518E-08 midg,1,midg; midg,igrid,midg 1.9827213E-09 1.6379731E-08 1,midg,midg; igrid,midg,midg 1.4310992E-08 5.0925539E-09 gauss-seidel spectral radius is 0.9874592 estimated iterations to convergence 73 setup time was (sec) 0.3500000 now iterating at: 07:53:57 rms-change max change #iterations 0.1441197 20.35942 at 10iterations 1.4590724E-02 2.303408 at 20iterations 1.5574550E-03 0.2437553 at 30iterations 1.7924169E-04 2.4831772E-02 at 40iterations 2.4109693E-05 3.5324097E-03 at 50iterations finished qdiffx linear iterations at : 07:54:00 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 2.4109693E-05 3.5324097E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 07:54:01 3.321u 0.196s 0:04.02 87.3% 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 07:54:01 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.929923 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): -1.551000 53.78800 ymin,ymax (A): -22.78400 22.90800 zmin,zma (A): 8.827000 53.88100 x,y,z range (A): 55.33900 45.69200 45.05400 scale (grids/A): 1.929923 object centre (A): 26.11850 6.1999321E-02 31.35400 number of atom coordinates read : 2380 total number of charged atoms : 2244 net assigned charge : 5.500007 assigned positive charge : 357.6723 centred at (gu) : 85.95480 90.97545 90.23418 assigned negative charge : -352.1728 centred at (gu) : 86.00835 90.80403 89.69182 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 71393 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19949 grid for indexing accessible points = 1.400000 m= 26318 mr = 50157 m= 4099 mr = 19714 m= 264 mr = 2488 m= 6 mr = 97 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 29624 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 169 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 17677 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) : 0.6433076 object centre at (A) : 26.11850 6.1999321E-02 31.35400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7079731E-02 4.0329240E-02 midg,1,midg; midg,igrid,midg -2.2339991E-03 5.5596926E-03 1,midg,midg; igrid,midg,midg 1.8690629E-02 2.5102140E-02 gauss-seidel spectral radius is 0.9986473 estimated iterations to convergence 215 setup time was (sec) 0.5800000 now iterating at: 07:54:02 rms-change max change #iterations 4.100368 173.6741 at 10iterations 1.925302 80.59651 at 20iterations 0.9128165 31.05394 at 30iterations 0.4308852 15.64565 at 40iterations 0.2025430 6.848476 at 50iterations 9.5310546E-02 2.942506 at 60iterations 4.4827208E-02 1.455879 at 70iterations 2.1094795E-02 0.6726685 at 80iterations 9.9440301E-03 0.3712158 at 90iterations 4.6955990E-03 0.1440282 at 100iterations 2.2051679E-03 7.0386767E-02 at 110iterations 1.0439205E-03 3.4530640E-02 at 120iterations finished qdiffx linear iterations at : 07:54:09 total time elapsed so far: 7.640000 # loops : 120 mean,max change (kT/e) : 1.0439205E-03 3.4530640E-02 energy calculations done at 7.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 07:54:09 7.784u 0.242s 0:08.34 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 07:54:09 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2380 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: 2.894884 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): -1.551000 53.78800 ymin,ymax (A): -22.78400 22.90800 zmin,zma (A): 8.827000 53.88100 x,y,z range (A): 55.33900 45.69200 45.05400 scale (grids/A): 2.894884 object centre (A): 26.11850 6.1999321E-02 31.35400 number of atom coordinates read : 2380 total number of charged atoms : 2244 net assigned charge : 5.500007 assigned positive charge : 357.6723 centred at (gu) : 83.93216 91.46305 90.35123 assigned negative charge : -352.1728 centred at (gu) : 84.01263 91.20612 89.53773 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 165032 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19949 grid for indexing accessible points = 1.400000 m= 85270 mr = 121170 m= 30982 mr = 70765 m= 7257 mr = 24901 m= 1077 mr = 5356 m= 65 mr = 697 m= 2 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9200000 number of dielectric boundary points 66773 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 17950 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) : 1.929923 object centre at (A) : 26.11850 6.1999321E-02 31.35400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2662569 0.4183761 midg,1,midg; midg,igrid,midg -2.6221029E-02 -2.2505721E-02 1,midg,midg; igrid,midg,midg 0.1260656 0.1712976 gauss-seidel spectral radius is 0.9992534 estimated iterations to convergence 289 setup time was (sec) 1.160000 now iterating at: 07:54:11 rms-change max change #iterations 9.541866 484.0691 at 10iterations 5.562234 158.8058 at 20iterations 3.223120 66.71813 at 30iterations 1.864794 37.82047 at 40iterations 1.077554 20.73603 at 50iterations 0.6187469 11.34911 at 60iterations 0.3564791 7.241773 at 70iterations 0.2044679 4.138000 at 80iterations 0.1176055 2.117753 at 90iterations 6.7454740E-02 1.204999 at 100iterations 3.8752045E-02 0.7263155 at 110iterations 2.2235103E-02 0.3813839 at 120iterations 1.2771676E-02 0.2447586 at 130iterations 7.3379423E-03 0.1444702 at 140iterations 4.2105038E-03 8.1933975E-02 at 150iterations 2.4283549E-03 4.3634415E-02 at 160iterations 1.4087720E-03 2.4139404E-02 at 170iterations 8.2048948E-04 1.6500473E-02 at 180iterations finished qdiffx linear iterations at : 07:54:22 total time elapsed so far: 12.38000 # loops : 180 mean,max change (kT/e) : 8.2048948E-04 1.6500473E-02 energy calculations done at 12.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.51000 DelPhi exited at 07:54:23 12.514u 0.213s 0:13.35 95.2% 0+0k 0+0io 0pf+0w