Mon Oct 10 17:00:55 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 Mon Oct 10 2011 at 17:00:55 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3340 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: 0.6468964 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): 13.10100 63.29500 ymin,ymax (A): -42.12600 9.779000 zmin,zma (A): 31.43900 86.47100 x,y,z range (A): 50.19400 51.90500 55.03200 scale (grids/A): 0.6468964 object centre (A): 38.19800 -16.17350 58.95500 number of atom coordinates read : 3340 total number of charged atoms : 3192 net assigned charge : 2.000039 assigned positive charge : 511.0386 centred at (gu) : 89.24110 90.95979 89.29683 assigned negative charge : -509.0395 centred at (gu) : 89.28886 90.92378 89.33407 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 9327 nv = 96 ne = 84 npr = 68351 no. pairs analyzed = 68351 no. exposed pairs = 3687 no. arc points = 25592 no. surface atoms = 1264 nbur = 2076 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 538 mr = 5556 m= 1 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 4222 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2472 ## 209 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 11188 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1805048E-08 -3.0171197E-09 midg,1,midg; midg,igrid,midg -2.6619404E-09 1.2195788E-08 1,midg,midg; igrid,midg,midg 1.4207735E-08 -4.6386432E-09 gauss-seidel spectral radius is 0.9876747 estimated iterations to convergence 74 setup time was (sec) 0.4700000 now iterating at: 17:00:56 rms-change max change #iterations 0.1804036 23.29875 at 10iterations 1.8716604E-02 2.501930 at 20iterations 2.2135833E-03 0.2820244 at 30iterations 4.6861754E-04 6.4306259E-02 at 40iterations 1.7922124E-04 2.4978638E-02 at 50iterations finished qdiffx linear iterations at : 17:00:59 total time elapsed so far: 3.600000 # loops : 50 mean,max change (kT/e) : 1.7922124E-04 2.4978638E-02 energy calculations done at 3.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.740000 DelPhi exited at 17:01:00 3.744u 0.211s 0:04.41 89.5% 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 Mon Oct 10 2011 at 17:01:00 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3340 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: 1.940689 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): 13.10100 63.29500 ymin,ymax (A): -42.12600 9.779000 zmin,zma (A): 31.43900 86.47100 x,y,z range (A): 50.19400 51.90500 55.03200 scale (grids/A): 1.940689 object centre (A): 38.19800 -16.17350 58.95500 number of atom coordinates read : 3340 total number of charged atoms : 3192 net assigned charge : 2.000039 assigned positive charge : 511.0386 centred at (gu) : 87.72221 92.87843 87.88956 assigned negative charge : -509.0395 centred at (gu) : 87.86630 92.77095 88.00188 start vw surface at 0.1000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 101187 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25592 grid for indexing accessible points = 1.400000 m= 40007 mr = 74192 m= 6903 mr = 30885 m= 524 mr = 4488 m= 7 mr = 225 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 542 time to turn everything in is 0.5000000 number of dielectric boundary points 38838 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 148 iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 25121 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) : 0.6468964 object centre at (A) : 38.19800 -16.17350 58.95500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0653870E-03 -1.6742861E-02 midg,1,midg; midg,igrid,midg 3.6894812E-03 3.1309303E-02 1,midg,midg; igrid,midg,midg 2.6557401E-02 3.7298493E-02 gauss-seidel spectral radius is 0.9987427 estimated iterations to convergence 223 setup time was (sec) 0.7400000 now iterating at: 17:01:01 rms-change max change #iterations 5.118810 189.6301 at 10iterations 2.477476 77.43440 at 20iterations 1.200602 33.40493 at 30iterations 0.5811738 17.16962 at 40iterations 0.2823503 7.482373 at 50iterations 0.1364967 3.918022 at 60iterations 6.6051893E-02 1.978086 at 70iterations 3.2087058E-02 0.9036751 at 80iterations 1.5622655E-02 0.4035988 at 90iterations 7.6560169E-03 0.2021599 at 100iterations 3.8204256E-03 0.1075706 at 110iterations 1.9748639E-03 6.2458038E-02 at 120iterations finished qdiffx linear iterations at : 17:01:08 total time elapsed so far: 8.050000 # loops : 120 mean,max change (kT/e) : 1.9748639E-03 6.2458038E-02 energy calculations done at 8.050000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.180000 DelPhi exited at 17:01:09 8.180u 0.314s 0:09.16 92.6% 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 17:01:09 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3340 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: 2.911034 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): 13.10100 63.29500 ymin,ymax (A): -42.12600 9.779000 zmin,zma (A): 31.43900 86.47100 x,y,z range (A): 50.19400 51.90500 55.03200 scale (grids/A): 2.911034 object centre (A): 38.19800 -16.17350 58.95500 number of atom coordinates read : 3340 total number of charged atoms : 3192 net assigned charge : 2.000039 assigned positive charge : 511.0386 centred at (gu) : 86.58313 94.31718 86.83401 assigned negative charge : -509.0395 centred at (gu) : 86.79947 94.15641 87.00265 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 233958 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25592 grid for indexing accessible points = 1.400000 m= 127794 mr = 178547 m= 49354 mr = 107984 m= 12650 mr = 40856 m= 2169 mr = 9673 m= 213 mr = 1464 m= 6 mr = 111 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 1750 time to turn everything in is 1.330000 number of dielectric boundary points 87509 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.450000 number of grid points assigned charge 25536 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) : 1.940689 object centre at (A) : 38.19800 -16.17350 58.95500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.8646539E-02 -8.8504426E-02 midg,1,midg; midg,igrid,midg -1.4911243E-02 0.3976073 1,midg,midg; igrid,midg,midg 0.2919697 0.4871177 gauss-seidel spectral radius is 0.9992929 estimated iterations to convergence 297 setup time was (sec) 1.620000 now iterating at: 17:01:11 rms-change max change #iterations 11.87218 465.9574 at 10iterations 7.056121 146.1795 at 20iterations 4.182800 81.42154 at 30iterations 2.470339 42.23668 at 40iterations 1.456491 24.99888 at 50iterations 0.8548323 14.43117 at 60iterations 0.5015025 9.307922 at 70iterations 0.2943032 4.519255 at 80iterations 0.1721406 2.755430 at 90iterations 0.1006663 1.694361 at 100iterations 5.8873780E-02 0.9916172 at 110iterations 3.4398872E-02 0.5482788 at 120iterations 2.0154322E-02 0.3424225 at 130iterations 1.1848417E-02 0.1884480 at 140iterations 6.9817412E-03 0.1077042 at 150iterations 4.1672694E-03 6.9776535E-02 at 160iterations 2.5406808E-03 4.4858932E-02 at 170iterations 1.6078262E-03 3.3920288E-02 at 180iterations finished qdiffx linear iterations at : 17:01:23 total time elapsed so far: 14.18000 # loops : 180 mean,max change (kT/e) : 1.6078262E-03 3.3920288E-02 energy calculations done at 14.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.31000 DelPhi exited at 17:01:24 14.312u 0.307s 0:15.39 94.9% 0+0k 0+0io 0pf+0w