Sat Oct 15 13:02:37 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 Sat Oct 15 2011 at 13:02:37 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 = 1367 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.8973357 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): -2.028000 37.64500 ymin,ymax (A): -14.37400 21.24400 zmin,zma (A): -14.66100 23.22900 x,y,z range (A): 39.67300 35.61800 37.89000 scale (grids/A): 0.8973357 object centre (A): 17.80850 3.435000 4.284000 number of atom coordinates read : 1367 total number of charged atoms : 1252 net assigned charge : 0.5000027 assigned positive charge : 203.9293 centred at (gu) : 89.95182 90.49003 90.96318 assigned negative charge : -203.4291 centred at (gu) : 89.66106 90.42329 91.16793 start vw surface at 5.9999999E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 7739 nv = 96 ne = 84 npr = 28775 no. pairs analyzed = 28775 no. exposed pairs = 1676 no. arc points = 12210 no. surface atoms = 562 nbur = 805 mkacc time = 4.9999997E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 786 mr = 4481 m= 12 mr = 262 m= 0 mr = 0 time to grow re-entrant surface = 5.9999995E-02 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.1300000 number of dielectric boundary points 3794 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 665 ## 63 charges are in solution ## iepsmp to db, and charging done at 0.1900000 number of grid points assigned charge 6604 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7222859E-06 -2.0209902E-06 midg,1,midg; midg,igrid,midg -4.0350710E-07 8.4306225E-07 1,midg,midg; igrid,midg,midg -2.5609163E-06 2.7420990E-06 gauss-seidel spectral radius is 0.9934360 estimated iterations to convergence 100 setup time was (sec) 0.3200000 now iterating at: 13:02:38 rms-change max change #iterations 0.3983133 56.70895 at 10iterations 7.6264739E-02 10.45063 at 20iterations 1.4335214E-02 1.768433 at 30iterations 2.6749936E-03 0.3289146 at 40iterations 5.0986302E-04 6.8933964E-02 at 50iterations finished qdiffx linear iterations at : 13:02:41 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 5.0986302E-04 6.8933964E-02 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 13:02:41 3.381u 0.187s 0:03.93 90.5% 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 15 2011 at 13:02:41 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 = 1367 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.692007 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): -2.028000 37.64500 ymin,ymax (A): -14.37400 21.24400 zmin,zma (A): -14.66100 23.22900 x,y,z range (A): 39.67300 35.61800 37.89000 scale (grids/A): 2.692007 object centre (A): 17.80850 3.435000 4.284000 number of atom coordinates read : 1367 total number of charged atoms : 1252 net assigned charge : 0.5000027 assigned positive charge : 203.9293 centred at (gu) : 89.85585 91.47028 92.88986 assigned negative charge : -203.4291 centred at (gu) : 88.98301 91.26997 93.50399 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 79272 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12210 grid for indexing accessible points = 1.400000 m= 37075 mr = 55357 m= 11849 mr = 29712 m= 2344 mr = 9030 m= 195 mr = 1629 m= 9 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 300 time to turn everything in is 0.4300000 number of dielectric boundary points 34928 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 10013 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) : 0.8973357 object centre at (A) : 17.80850 3.435000 4.284000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.9525558E-02 1.2487076E-02 midg,1,midg; midg,igrid,midg -6.2777378E-02 -8.0308460E-02 1,midg,midg; igrid,midg,midg 2.3000874E-02 0.1145785 gauss-seidel spectral radius is 0.9991328 estimated iterations to convergence 268 setup time was (sec) 0.6400000 now iterating at: 13:02:42 rms-change max change #iterations 5.404094 228.9988 at 10iterations 2.972520 99.03687 at 20iterations 1.626101 45.10069 at 30iterations 0.8870933 27.30719 at 40iterations 0.4844024 14.42896 at 50iterations 0.2657984 7.013387 at 60iterations 0.1450946 3.704401 at 70iterations 7.9390220E-02 2.217554 at 80iterations 4.3293059E-02 1.218559 at 90iterations 2.3603452E-02 0.6361334 at 100iterations 1.2942050E-02 0.3568277 at 110iterations 7.0361733E-03 0.1786423 at 120iterations finished qdiffx linear iterations at : 13:02:49 total time elapsed so far: 7.620000 # loops : 120 mean,max change (kT/e) : 7.0361733E-03 0.1786423 energy calculations done at 7.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 13:02:50 7.755u 0.199s 0:08.28 95.8% 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 15 2011 at 13:02:50 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 = 1367 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 4.038011 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): -2.028000 37.64500 ymin,ymax (A): -14.37400 21.24400 zmin,zma (A): -14.66100 23.22900 x,y,z range (A): 39.67300 35.61800 37.89000 scale (grids/A): 4.038011 object centre (A): 17.80850 3.435000 4.284000 number of atom coordinates read : 1367 total number of charged atoms : 1252 net assigned charge : 0.5000027 assigned positive charge : 203.9293 centred at (gu) : 89.78378 92.20552 94.33482 assigned negative charge : -203.4291 centred at (gu) : 88.47459 91.90498 95.25601 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 181452 reading accessible surface arcs data from file ARCDAT no. of arc points read = 12210 grid for indexing accessible points = 1.400000 m= 105223 mr = 131881 m= 56633 mr = 89744 m= 24524 mr = 49212 m= 8330 mr = 20477 m= 2197 mr = 6759 m= 290 mr = 1717 m= 14 mr = 181 m= 0 mr = 2 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 915 time to turn everything in is 1.380000 number of dielectric boundary points 78690 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 10016 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) : 2.692007 object centre at (A) : 17.80850 3.435000 4.284000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5124002 0.1612956 midg,1,midg; midg,igrid,midg -0.3682585 -0.6569246 1,midg,midg; igrid,midg,midg 0.6270896 0.4890369 gauss-seidel spectral radius is 0.9993446 estimated iterations to convergence 308 setup time was (sec) 1.630000 now iterating at: 13:02:52 rms-change max change #iterations 10.89789 212.6664 at 10iterations 6.454342 121.8583 at 20iterations 3.821894 67.39082 at 30iterations 2.266327 34.52163 at 40iterations 1.345246 21.42356 at 50iterations 0.7987262 13.51810 at 60iterations 0.4741000 7.332790 at 70iterations 0.2813997 4.307985 at 80iterations 0.1666331 2.470056 at 90iterations 9.9056840E-02 1.535069 at 100iterations 5.8767959E-02 0.8438911 at 110iterations 3.5034079E-02 0.5357094 at 120iterations 2.0968884E-02 0.3173628 at 130iterations 1.2546561E-02 0.1837540 at 140iterations 7.5951968E-03 0.1256790 at 150iterations 4.6581263E-03 7.6900482E-02 at 160iterations 2.9262051E-03 5.9333801E-02 at 170iterations 1.9029201E-03 3.8112640E-02 at 180iterations finished qdiffx linear iterations at : 13:03:03 total time elapsed so far: 13.26000 # loops : 180 mean,max change (kT/e) : 1.9029201E-03 3.8112640E-02 energy calculations done at 13.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.39000 DelPhi exited at 13:03:04 13.394u 0.234s 0:14.06 96.8% 0+0k 0+0io 0pf+0w