Sun Oct 9 13:07:37 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+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 Sun Oct 9 2011 at 13:07:37 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2365 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: 0.6916248 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): -6.858000 44.61500 ymin,ymax (A): -14.09200 36.54400 zmin,zma (A): 2.076000 45.53700 x,y,z range (A): 51.47300 50.63600 43.46100 scale (grids/A): 0.6916248 object centre (A): 18.87850 11.22600 23.80650 number of atom coordinates read : 2365 total number of charged atoms : 2225 net assigned charge : 4.500012 assigned positive charge : 362.9972 centred at (gu) : 89.58285 91.35428 90.47255 assigned negative charge : -358.4976 centred at (gu) : 89.62848 91.48026 90.50536 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7754 nv = 96 ne = 84 npr = 46925 no. pairs analyzed = 46925 no. exposed pairs = 3003 no. arc points = 21287 no. surface atoms = 1015 nbur = 1350 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 485 mr = 4263 m= 1 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3900 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2002 ## 193 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8715 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.6067554E-08 1.4854194E-08 midg,1,midg; midg,igrid,midg 5.7961852E-08 -3.1989806E-08 1,midg,midg; igrid,midg,midg 4.8410843E-08 7.9485174E-09 gauss-seidel spectral radius is 0.9891406 estimated iterations to convergence 78 setup time was (sec) 0.3800000 now iterating at: 13:07:37 rms-change max change #iterations 0.1969944 26.97402 at 10iterations 2.3584539E-02 3.552967 at 20iterations 3.2943196E-03 0.5257988 at 30iterations 7.2244374E-04 0.1274567 at 40iterations 2.3915459E-04 3.8928986E-02 at 50iterations finished qdiffx linear iterations at : 13:07:40 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 2.3915459E-04 3.8928986E-02 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 13:07:41 3.391u 0.171s 0:03.83 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 Sun Oct 9 2011 at 13:07:41 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2365 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: 2.074874 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): -6.858000 44.61500 ymin,ymax (A): -14.09200 36.54400 zmin,zma (A): 2.076000 45.53700 x,y,z range (A): 51.47300 50.63600 43.46100 scale (grids/A): 2.074874 object centre (A): 18.87850 11.22600 23.80650 number of atom coordinates read : 2365 total number of charged atoms : 2225 net assigned charge : 4.500012 assigned positive charge : 362.9972 centred at (gu) : 88.74831 94.06248 91.41718 assigned negative charge : -358.4976 centred at (gu) : 88.88528 94.44045 91.51589 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 82400 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21287 grid for indexing accessible points = 1.400000 m= 31487 mr = 57183 m= 5451 mr = 23177 m= 457 mr = 3331 m= 21 mr = 238 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 35887 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 127 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 17633 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) : 0.6916248 object centre at (A) : 18.87850 11.22600 23.80650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4052319E-02 1.3112454E-02 midg,1,midg; midg,igrid,midg 1.5844766E-02 -1.9515755E-02 1,midg,midg; igrid,midg,midg 4.9785722E-02 -2.8453302E-02 gauss-seidel spectral radius is 0.9988225 estimated iterations to convergence 231 setup time was (sec) 0.6200000 now iterating at: 13:07:41 rms-change max change #iterations 4.858600 219.5866 at 10iterations 2.383132 83.38298 at 20iterations 1.176720 36.77068 at 30iterations 0.5848439 16.80309 at 40iterations 0.2874676 8.257339 at 50iterations 0.1422023 4.440709 at 60iterations 7.0678711E-02 2.102612 at 70iterations 3.5078228E-02 1.006129 at 80iterations 1.7425841E-02 0.5713024 at 90iterations 8.7940432E-03 0.2853889 at 100iterations 4.5222118E-03 0.1312981 at 110iterations 2.4049878E-03 8.3776474E-02 at 120iterations finished qdiffx linear iterations at : 13:07:48 total time elapsed so far: 7.750000 # loops : 120 mean,max change (kT/e) : 2.4049878E-03 8.3776474E-02 energy calculations done at 7.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.890000 DelPhi exited at 13:07:49 7.888u 0.198s 0:08.41 95.9% 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 Sun Oct 9 2011 at 13:07:49 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2365 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: 3.112311 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): -6.858000 44.61500 ymin,ymax (A): -14.09200 36.54400 zmin,zma (A): 2.076000 45.53700 x,y,z range (A): 51.47300 50.63600 43.46100 scale (grids/A): 3.112311 object centre (A): 18.87850 11.22600 23.80650 number of atom coordinates read : 2365 total number of charged atoms : 2225 net assigned charge : 4.500012 assigned positive charge : 362.9972 centred at (gu) : 88.12236 96.09357 92.12569 assigned negative charge : -358.4976 centred at (gu) : 88.32778 96.66063 92.27365 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 189918 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21287 grid for indexing accessible points = 1.400000 m= 99567 mr = 137877 m= 38345 mr = 81574 m= 9963 mr = 30771 m= 1792 mr = 7334 m= 255 mr = 1213 m= 11 mr = 187 m= 0 mr = 2 time to grow re-entrant surface = 0.6300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.250000 number of dielectric boundary points 80893 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 17794 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) : 2.074874 object centre at (A) : 18.87850 11.22600 23.80650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5091100 3.8566120E-02 midg,1,midg; midg,igrid,midg 0.3295499 -0.1738505 1,midg,midg; igrid,midg,midg 0.6216753 -0.6423067 gauss-seidel spectral radius is 0.9992980 estimated iterations to convergence 298 setup time was (sec) 1.490000 now iterating at: 13:07:51 rms-change max change #iterations 10.90387 411.8941 at 10iterations 6.490434 146.6516 at 20iterations 3.846106 67.98444 at 30iterations 2.275872 41.88343 at 40iterations 1.346475 23.47299 at 50iterations 0.7928906 14.66478 at 60iterations 0.4662530 10.68143 at 70iterations 0.2734276 4.671854 at 80iterations 0.1608198 2.669605 at 90iterations 9.4311312E-02 1.622010 at 100iterations 5.5385243E-02 1.011726 at 110iterations 3.2641809E-02 0.5876236 at 120iterations 1.9363439E-02 0.3615952 at 130iterations 1.1661863E-02 0.2271881 at 140iterations 7.1935412E-03 0.1515083 at 150iterations 4.6286904E-03 0.1047897 at 160iterations 3.1642013E-03 6.6150665E-02 at 170iterations 2.3044574E-03 4.9106598E-02 at 180iterations finished qdiffx linear iterations at : 13:08:02 total time elapsed so far: 12.96000 # loops : 180 mean,max change (kT/e) : 2.3044574E-03 4.9106598E-02 energy calculations done at 12.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.09000 DelPhi exited at 13:08:03 13.091u 0.192s 0:13.57 97.8% 0+0k 0+0io 0pf+0w