Mon Oct 10 01:00:12 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 Mon Oct 10 2011 at 01:00:12 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 = 1964 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: 0.6185603 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): -35.51600 10.13400 ymin,ymax (A): 1.851000 42.10800 zmin,zma (A): -27.65100 29.90200 x,y,z range (A): 45.65000 40.25700 57.55300 scale (grids/A): 0.6185603 object centre (A): -12.69100 21.97950 1.125501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.7721 centred at (gu) : 90.43597 89.25272 89.98291 assigned negative charge : -284.7723 centred at (gu) : 90.35195 89.39922 89.98170 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5252 nv = 96 ne = 84 npr = 39332 no. pairs analyzed = 39332 no. exposed pairs = 2542 no. arc points = 17430 no. surface atoms = 859 nbur = 1105 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 296 mr = 2900 m= 4 mr = 53 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 2599 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1803 ## 181 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 6251 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1922755E-09 2.2887789E-09 midg,1,midg; midg,igrid,midg 1.0611321E-08 -3.9804786E-09 1,midg,midg; igrid,midg,midg -1.5551009E-09 6.7553896E-09 gauss-seidel spectral radius is 0.9864144 estimated iterations to convergence 70 setup time was (sec) 0.4900000 now iterating at: 01:00:13 rms-change max change #iterations 0.1065100 20.75345 at 10iterations 9.6901106E-03 1.688271 at 20iterations 8.9085556E-04 0.1345215 at 30iterations 8.0209800E-05 1.1764526E-02 at 40iterations 7.1986437E-06 1.2502670E-03 at 50iterations finished qdiffx linear iterations at : 01:00:16 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 7.1986437E-06 1.2502670E-03 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 01:00:17 3.545u 0.233s 0:04.13 91.2% 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 Mon Oct 10 2011 at 01:00:17 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 = 1964 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: 1.855681 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): -35.51600 10.13400 ymin,ymax (A): 1.851000 42.10800 zmin,zma (A): -27.65100 29.90200 x,y,z range (A): 45.65000 40.25700 57.55300 scale (grids/A): 1.855681 object centre (A): -12.69100 21.97950 1.125501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.7721 centred at (gu) : 91.30801 87.75831 89.94884 assigned negative charge : -284.7723 centred at (gu) : 91.05613 88.19781 89.94523 start vw surface at 0.1400000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 55751 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17430 grid for indexing accessible points = 1.400000 m= 22298 mr = 38362 m= 3738 mr = 17116 m= 175 mr = 2487 m= 0 mr = 48 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 292 time to turn everything in is 0.4600000 number of dielectric boundary points 23949 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 128 iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 14368 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) : 0.6185603 object centre at (A) : -12.69100 21.97950 1.125501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9008338E-02 2.0601775E-02 midg,1,midg; midg,igrid,midg 2.9247447E-03 -7.8792246E-03 1,midg,midg; igrid,midg,midg -3.8201741E-03 -1.6204164E-03 gauss-seidel spectral radius is 0.9984922 estimated iterations to convergence 204 setup time was (sec) 0.7800000 now iterating at: 01:00:18 rms-change max change #iterations 3.424548 162.8385 at 10iterations 1.538513 57.73623 at 20iterations 0.6924992 27.13617 at 30iterations 0.3123049 11.88231 at 40iterations 0.1404006 5.144196 at 50iterations 6.2817156E-02 2.583807 at 60iterations 2.8366523E-02 1.058282 at 70iterations 1.2808504E-02 0.4886093 at 80iterations 5.7576713E-03 0.2118988 at 90iterations 2.5985341E-03 8.7306976E-02 at 100iterations 1.1721220E-03 4.0776730E-02 at 110iterations 5.2828941E-04 1.8618584E-02 at 120iterations finished qdiffx linear iterations at : 01:00:25 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 5.2828941E-04 1.8618584E-02 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.960000 DelPhi exited at 01:00:25 7.964u 0.234s 0:08.62 95.0% 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 Mon Oct 10 2011 at 01:00:25 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 = 1964 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: 2.783521 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): -35.51600 10.13400 ymin,ymax (A): 1.851000 42.10800 zmin,zma (A): -27.65100 29.90200 x,y,z range (A): 45.65000 40.25700 57.55300 scale (grids/A): 2.783521 object centre (A): -12.69100 21.97950 1.125501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.7721 centred at (gu) : 91.96204 86.63756 89.92327 assigned negative charge : -284.7723 centred at (gu) : 91.58418 87.29683 89.91785 start vw surface at 0.1400000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 128293 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17430 grid for indexing accessible points = 1.400000 m= 69202 mr = 92333 m= 28054 mr = 57599 m= 7023 mr = 23457 m= 825 mr = 5485 m= 22 mr = 501 m= 0 mr = 4 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 1008 time to turn everything in is 1.120000 number of dielectric boundary points 54040 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 14656 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) : 1.855681 object centre at (A) : -12.69100 21.97950 1.125501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9514765E-02 3.5546120E-02 midg,1,midg; midg,igrid,midg -2.4565816E-02 -0.1002372 1,midg,midg; igrid,midg,midg -5.4848507E-02 -6.9042161E-02 gauss-seidel spectral radius is 0.9992026 estimated iterations to convergence 280 setup time was (sec) 1.450000 now iterating at: 01:00:27 rms-change max change #iterations 8.198611 319.3835 at 10iterations 4.734168 119.7575 at 20iterations 2.693925 68.46314 at 30iterations 1.531091 35.26987 at 40iterations 0.8698210 20.24829 at 50iterations 0.4911005 10.51931 at 60iterations 0.2771687 5.945999 at 70iterations 0.1566355 3.224868 at 80iterations 8.8250220E-02 1.958855 at 90iterations 4.9768783E-02 1.055858 at 100iterations 2.8025173E-02 0.6089382 at 110iterations 1.5780387E-02 0.3226414 at 120iterations 8.8818008E-03 0.1763496 at 130iterations 4.9901074E-03 0.1045666 at 140iterations 2.8034816E-03 6.2230766E-02 at 150iterations 1.5776549E-03 3.4514427E-02 at 160iterations 8.8563090E-04 1.7652512E-02 at 170iterations 4.9902155E-04 1.0717392E-02 at 180iterations finished qdiffx linear iterations at : 01:00:38 total time elapsed so far: 12.55000 # loops : 180 mean,max change (kT/e) : 4.9902155E-04 1.0717392E-02 energy calculations done at 12.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.76000 DelPhi exited at 01:00:39 12.759u 0.266s 0:13.29 97.8% 0+0k 0+0io 0pf+0w