Sat Oct 8 19:50:55 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 Sat Oct 8 2011 at 19:50:55 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2621 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN7 729 has a net charge of 1.4000 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: 0.6142272 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): -32.14400 17.69900 ymin,ymax (A): -23.52500 22.88600 zmin,zma (A): -12.56800 45.39100 x,y,z range (A): 49.84300 46.41100 57.95900 scale (grids/A): 0.6142272 object centre (A): -7.222501 -0.3195000 16.41150 number of atom coordinates read : 2621 total number of charged atoms : 2475 net assigned charge : 3.500007 assigned positive charge : 397.0500 centred at (gu) : 88.72446 89.28497 89.63150 assigned negative charge : -393.5505 centred at (gu) : 88.62948 89.35039 89.52356 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6424 nv = 96 ne = 84 npr = 54921 no. pairs analyzed = 54921 no. exposed pairs = 3028 no. arc points = 21753 no. surface atoms = 1012 nbur = 1609 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 313 mr = 3548 m= 2 mr = 37 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 95 time to turn everything in is 0.2000000 number of dielectric boundary points 3154 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2241 ## 237 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 8050 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.1117700E-09 7.8202191E-09 midg,1,midg; midg,igrid,midg 7.1786852E-09 -1.0968727E-09 1,midg,midg; igrid,midg,midg -4.0878056E-09 5.8605520E-09 gauss-seidel spectral radius is 0.9862738 estimated iterations to convergence 70 setup time was (sec) 0.4300000 now iterating at: 19:50:55 rms-change max change #iterations 0.1201281 21.60495 at 10iterations 1.0784876E-02 1.582241 at 20iterations 9.6752879E-04 0.1574764 at 30iterations 8.9324341E-05 1.2870789E-02 at 40iterations 7.9853407E-06 1.0786057E-03 at 50iterations finished qdiffx linear iterations at : 19:50:59 total time elapsed so far: 3.670000 # loops : 50 mean,max change (kT/e) : 7.9853407E-06 1.0786057E-03 energy calculations done at 3.670000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.810000 DelPhi exited at 19:50:59 3.814u 0.211s 0:04.29 93.7% 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 Sat Oct 8 2011 at 19:50:59 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2621 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN7 729 has a net charge of 1.4000 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: 1.842682 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): -32.14400 17.69900 ymin,ymax (A): -23.52500 22.88600 zmin,zma (A): -12.56800 45.39100 x,y,z range (A): 49.84300 46.41100 57.95900 scale (grids/A): 1.842682 object centre (A): -7.222501 -0.3195000 16.41150 number of atom coordinates read : 2621 total number of charged atoms : 2475 net assigned charge : 3.500007 assigned positive charge : 397.0500 centred at (gu) : 86.17314 87.85448 88.89396 assigned negative charge : -393.5505 centred at (gu) : 85.88811 88.05099 88.57059 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 70484 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21753 grid for indexing accessible points = 1.400000 m= 24094 mr = 49291 m= 3235 mr = 17652 m= 146 mr = 1971 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 6365 time to turn everything in is 0.3600000 number of dielectric boundary points 29010 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 219 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 19418 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) : 0.6142272 object centre at (A) : -7.222501 -0.3195000 16.41150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3317709E-02 2.7361525E-02 midg,1,midg; midg,igrid,midg 1.3160381E-02 -2.6442937E-03 1,midg,midg; igrid,midg,midg -4.9619889E-03 3.1965028E-02 gauss-seidel spectral radius is 0.9985448 estimated iterations to convergence 208 setup time was (sec) 0.6300000 now iterating at: 19:51:00 rms-change max change #iterations 4.011273 158.1368 at 10iterations 1.831812 64.69422 at 20iterations 0.8387642 27.10142 at 30iterations 0.3828832 13.59498 at 40iterations 0.1750121 5.975449 at 50iterations 8.0183938E-02 2.720680 at 60iterations 3.6630768E-02 1.179680 at 70iterations 1.6741492E-02 0.5118279 at 80iterations 7.6439790E-03 0.2499390 at 90iterations 3.4948362E-03 0.1183815 at 100iterations 1.6046278E-03 5.2200317E-02 at 110iterations 7.3140714E-04 2.4789333E-02 at 120iterations finished qdiffx linear iterations at : 19:51:08 total time elapsed so far: 8.930000 # loops : 120 mean,max change (kT/e) : 7.3140714E-04 2.4789333E-02 energy calculations done at 8.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.060000 DelPhi exited at 19:51:09 9.060u 0.287s 0:09.65 96.7% 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 Sat Oct 8 2011 at 19:51:09 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2621 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN7 729 has a net charge of 1.4000 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: 2.764023 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): -32.14400 17.69900 ymin,ymax (A): -23.52500 22.88600 zmin,zma (A): -12.56800 45.39100 x,y,z range (A): 49.84300 46.41100 57.95900 scale (grids/A): 2.764023 object centre (A): -7.222501 -0.3195000 16.41150 number of atom coordinates read : 2621 total number of charged atoms : 2475 net assigned charge : 3.500007 assigned positive charge : 397.0500 centred at (gu) : 84.25954 86.78150 88.34100 assigned negative charge : -393.5505 centred at (gu) : 83.83212 87.07643 87.85569 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 163292 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21753 grid for indexing accessible points = 1.400000 m= 80055 mr = 119327 m= 26226 mr = 65653 m= 5464 mr = 20802 m= 630 mr = 4043 m= 16 mr = 417 m= 0 mr = 3 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 21450 time to turn everything in is 0.9100000 number of dielectric boundary points 65438 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 19794 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) : 1.842682 object centre at (A) : -7.222501 -0.3195000 16.41150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0172542E-02 0.3770898 midg,1,midg; midg,igrid,midg 0.1560618 -3.2527603E-02 1,midg,midg; igrid,midg,midg -4.7485873E-02 0.4260235 gauss-seidel spectral radius is 0.9992287 estimated iterations to convergence 284 setup time was (sec) 1.160000 now iterating at: 19:51:10 rms-change max change #iterations 9.473227 258.7576 at 10iterations 5.438762 113.4281 at 20iterations 3.108306 71.71651 at 30iterations 1.769947 38.55598 at 40iterations 1.009356 21.36006 at 50iterations 0.5744202 13.67543 at 60iterations 0.3261348 7.180894 at 70iterations 0.1852256 3.848213 at 80iterations 0.1054801 1.987753 at 90iterations 5.9771515E-02 1.082001 at 100iterations 3.3930790E-02 0.6739960 at 110iterations 1.9261764E-02 0.3841639 at 120iterations 1.0926053E-02 0.2075968 at 130iterations 6.2150583E-03 0.1277294 at 140iterations 3.5181723E-03 6.2612534E-02 at 150iterations 1.9980527E-03 4.2375565E-02 at 160iterations 1.1342224E-03 1.9248009E-02 at 170iterations 6.4259383E-04 1.2157440E-02 at 180iterations finished qdiffx linear iterations at : 19:51:22 total time elapsed so far: 13.25000 # loops : 180 mean,max change (kT/e) : 6.4259383E-04 1.2157440E-02 energy calculations done at 13.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.38000 DelPhi exited at 19:51:23 13.382u 0.247s 0:13.89 98.0% 0+0k 0+0io 0pf+0w