Sat Oct 8 15:51:29 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 8 2011 at 15:51:29 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 = 2294 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6526362 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): -1.516000 45.59900 ymin,ymax (A): -17.16400 29.20000 zmin,zma (A): -17.74700 36.80100 x,y,z range (A): 47.11500 46.36400 54.54800 scale (grids/A): 0.6526362 object centre (A): 22.04150 6.018000 9.526999 number of atom coordinates read : 2294 total number of charged atoms : 2232 net assigned charge : 3.000002 assigned positive charge : 342.4212 centred at (gu) : 90.51765 88.85439 90.06517 assigned negative charge : -339.4218 centred at (gu) : 90.50436 88.97534 90.12213 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6722 nv = 96 ne = 84 npr = 45716 no. pairs analyzed = 45716 no. exposed pairs = 2900 no. arc points = 20293 no. surface atoms = 986 nbur = 1308 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 385 mr = 3726 m= 1 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3323 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2001 ## 183 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8032 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3910139E-08 -2.2100715E-09 midg,1,midg; midg,igrid,midg 2.9438636E-08 -8.9359737E-09 1,midg,midg; igrid,midg,midg 3.7147081E-09 8.7983087E-09 gauss-seidel spectral radius is 0.9878091 estimated iterations to convergence 74 setup time was (sec) 0.6100000 now iterating at: 15:51:30 rms-change max change #iterations 0.1464083 22.80825 at 10iterations 1.5240968E-02 2.179432 at 20iterations 1.6147223E-03 0.2061806 at 30iterations 1.8980612E-04 2.7930260E-02 at 40iterations 3.3494023E-05 4.7684908E-03 at 50iterations finished qdiffx linear iterations at : 15:51:33 total time elapsed so far: 4.000000 # loops : 50 mean,max change (kT/e) : 3.3494023E-05 4.7684908E-03 energy calculations done at 4.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.180000 DelPhi exited at 15:51:33 4.186u 0.276s 0:04.79 92.9% 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 Sat Oct 8 2011 at 15:51:34 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 = 2294 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.957909 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): -1.516000 45.59900 ymin,ymax (A): -17.16400 29.20000 zmin,zma (A): -17.74700 36.80100 x,y,z range (A): 47.11500 46.36400 54.54800 scale (grids/A): 1.957909 object centre (A): 22.04150 6.018000 9.526999 number of atom coordinates read : 2294 total number of charged atoms : 2232 net assigned charge : 3.000002 assigned positive charge : 342.4212 centred at (gu) : 91.55259 86.56265 90.19508 assigned negative charge : -339.4218 centred at (gu) : 91.51279 86.92594 90.36629 start vw surface at 0.1400000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 72088 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20293 grid for indexing accessible points = 1.400000 m= 26892 mr = 50160 m= 4746 mr = 20119 m= 345 mr = 3199 m= 7 mr = 148 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 454 time to turn everything in is 0.6400000 number of dielectric boundary points 30452 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 134 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 17614 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) : 0.6526362 object centre at (A) : 22.04150 6.018000 9.526999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5952747E-02 1.0926684E-02 midg,1,midg; midg,igrid,midg 2.4264868E-02 -5.4337890E-03 1,midg,midg; igrid,midg,midg -3.8107219E-03 -4.2665988E-02 gauss-seidel spectral radius is 0.9986790 estimated iterations to convergence 218 setup time was (sec) 0.9400000 now iterating at: 15:51:35 rms-change max change #iterations 4.179559 205.4933 at 10iterations 1.980635 70.76480 at 20iterations 0.9414545 33.34436 at 30iterations 0.4485875 13.90878 at 40iterations 0.2122005 7.033539 at 50iterations 0.1011595 3.218611 at 60iterations 4.8130181E-02 1.585449 at 70iterations 2.2755520E-02 0.7639599 at 80iterations 1.0854853E-02 0.3426981 at 90iterations 5.1639080E-03 0.1632538 at 100iterations 2.4603794E-03 7.9269409E-02 at 110iterations 1.1704555E-03 4.2029381E-02 at 120iterations finished qdiffx linear iterations at : 15:51:43 total time elapsed so far: 9.530000 # loops : 120 mean,max change (kT/e) : 1.1704555E-03 4.2029381E-02 energy calculations done at 9.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.720000 DelPhi exited at 15:51:44 9.718u 0.348s 0:10.36 97.0% 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 15:51:44 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 = 2294 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.936863 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): -1.516000 45.59900 ymin,ymax (A): -17.16400 29.20000 zmin,zma (A): -17.74700 36.80100 x,y,z range (A): 47.11500 46.36400 54.54800 scale (grids/A): 2.936863 object centre (A): 22.04150 6.018000 9.526999 number of atom coordinates read : 2294 total number of charged atoms : 2232 net assigned charge : 3.000002 assigned positive charge : 342.4212 centred at (gu) : 92.32873 84.84377 90.29240 assigned negative charge : -339.4218 centred at (gu) : 92.26914 85.38886 90.54949 start vw surface at 0.1500000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 166568 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20293 grid for indexing accessible points = 1.400000 m= 85171 mr = 121516 m= 33045 mr = 69891 m= 8842 mr = 27118 m= 1424 mr = 6944 m= 96 mr = 1012 m= 2 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 1610 time to turn everything in is 1.680000 number of dielectric boundary points 68629 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 17854 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) : 1.957909 object centre at (A) : 22.04150 6.018000 9.526999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2708535 0.1103671 midg,1,midg; midg,igrid,midg 0.1822234 -7.0759997E-02 1,midg,midg; igrid,midg,midg 1.7247722E-03 -0.5747342 gauss-seidel spectral radius is 0.9992699 estimated iterations to convergence 292 setup time was (sec) 2.020000 now iterating at: 15:51:46 rms-change max change #iterations 9.791973 505.4490 at 10iterations 5.752070 137.5320 at 20iterations 3.364630 68.95456 at 30iterations 1.970736 38.41231 at 40iterations 1.147656 22.22594 at 50iterations 0.6685654 13.04631 at 60iterations 0.3884997 7.070821 at 70iterations 0.2250194 4.426123 at 80iterations 0.1304308 2.524521 at 90iterations 7.5469896E-02 1.416391 at 100iterations 4.3732841E-02 0.7896562 at 110iterations 2.5228584E-02 0.5005693 at 120iterations 1.4602358E-02 0.2688370 at 130iterations 8.4240846E-03 0.1688366 at 140iterations 4.8714643E-03 9.2740059E-02 at 150iterations 2.8158117E-03 5.2345276E-02 at 160iterations 1.6224652E-03 3.0216217E-02 at 170iterations 9.3845796E-04 1.7084122E-02 at 180iterations finished qdiffx linear iterations at : 15:52:00 total time elapsed so far: 16.19000 # loops : 180 mean,max change (kT/e) : 9.3845796E-04 1.7084122E-02 energy calculations done at 16.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.37000 DelPhi exited at 15:52:01 16.374u 0.333s 0:17.00 98.2% 0+0k 0+0io 0pf+0w