Mon Oct 10 14:01:28 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 14:01:29 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2214 !!! WARNING: NAP 207 has a net charge of -2.0000 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: 0.7052438 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): -16.41400 30.51400 ymin,ymax (A): -19.26900 31.21000 zmin,zma (A): -4.850000 34.89400 x,y,z range (A): 46.92800 50.47900 39.74400 scale (grids/A): 0.7052438 object centre (A): 7.050000 5.970500 15.02200 number of atom coordinates read : 2214 total number of charged atoms : 2077 net assigned charge : 7.000020 assigned positive charge : 334.6884 centred at (gu) : 90.09204 90.69715 90.93748 assigned negative charge : -327.6889 centred at (gu) : 90.00780 90.76534 91.05180 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7441 nv = 96 ne = 84 npr = 45362 no. pairs analyzed = 45362 no. exposed pairs = 2969 no. arc points = 20810 no. surface atoms = 998 nbur = 1216 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 535 mr = 3927 m= 8 mr = 94 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3963 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1891 ## 170 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 8315 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.4022752E-08 -1.0359938E-09 midg,1,midg; midg,igrid,midg 7.9005090E-08 2.5901789E-08 1,midg,midg; igrid,midg,midg 1.4720045E-08 9.9897051E-08 gauss-seidel spectral radius is 0.9895414 estimated iterations to convergence 80 setup time was (sec) 0.6400000 now iterating at: 14:01:30 rms-change max change #iterations 0.2050731 29.92586 at 10iterations 2.4885442E-02 3.663794 at 20iterations 3.0340096E-03 0.4192867 at 30iterations 3.7797107E-04 4.7815323E-02 at 40iterations 4.6306897E-05 6.9580078E-03 at 50iterations finished qdiffx linear iterations at : 14:01:33 total time elapsed so far: 4.130000 # loops : 50 mean,max change (kT/e) : 4.6306897E-05 6.9580078E-03 energy calculations done at 4.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.320000 DelPhi exited at 14:01:34 4.324u 0.262s 0:05.51 83.1% 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 14:01:34 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2214 !!! WARNING: NAP 207 has a net charge of -2.0000 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: 2.115731 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): -16.41400 30.51400 ymin,ymax (A): -19.26900 31.21000 zmin,zma (A): -4.850000 34.89400 x,y,z range (A): 46.92800 50.47900 39.74400 scale (grids/A): 2.115731 object centre (A): 7.050000 5.970500 15.02200 number of atom coordinates read : 2214 total number of charged atoms : 2077 net assigned charge : 7.000020 assigned positive charge : 334.6884 centred at (gu) : 90.27611 92.09126 92.81247 assigned negative charge : -327.6889 centred at (gu) : 90.02335 92.29599 93.15530 start vw surface at 0.1700000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 77929 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20810 grid for indexing accessible points = 1.400000 m= 30660 mr = 52225 m= 6395 mr = 22674 m= 679 mr = 4187 m= 20 mr = 313 m= 0 mr = 1 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 127 time to turn everything in is 0.7300000 number of dielectric boundary points 36283 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 96 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 16513 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) : 0.7052438 object centre at (A) : 7.050000 5.970500 15.02200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.5609768E-02 8.5058305E-03 midg,1,midg; midg,igrid,midg 2.8718293E-02 2.2424627E-02 1,midg,midg; igrid,midg,midg -1.4829696E-03 5.1750846E-02 gauss-seidel spectral radius is 0.9988490 estimated iterations to convergence 233 setup time was (sec) 1.050000 now iterating at: 14:01:36 rms-change max change #iterations 4.753549 250.6231 at 10iterations 2.352475 88.61364 at 20iterations 1.168431 36.16012 at 30iterations 0.5818138 20.51942 at 40iterations 0.2894636 8.450734 at 50iterations 0.1443372 4.221155 at 60iterations 7.1709357E-02 2.130917 at 70iterations 3.5685681E-02 1.101353 at 80iterations 1.7724469E-02 0.5493317 at 90iterations 8.8101756E-03 0.2557983 at 100iterations 4.3982966E-03 0.1225834 at 110iterations 2.1895189E-03 6.3703060E-02 at 120iterations finished qdiffx linear iterations at : 14:01:45 total time elapsed so far: 10.05000 # loops : 120 mean,max change (kT/e) : 2.1895189E-03 6.3703060E-02 energy calculations done at 10.05000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.22000 DelPhi exited at 14:01:46 10.226u 0.325s 0:11.27 93.5% 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 14:01:46 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2214 !!! WARNING: NAP 207 has a net charge of -2.0000 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: 3.173597 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): -16.41400 30.51400 ymin,ymax (A): -19.26900 31.21000 zmin,zma (A): -4.850000 34.89400 x,y,z range (A): 46.92800 50.47900 39.74400 scale (grids/A): 3.173597 object centre (A): 7.050000 5.970500 15.02200 number of atom coordinates read : 2214 total number of charged atoms : 2077 net assigned charge : 7.000020 assigned positive charge : 334.6884 centred at (gu) : 90.41404 93.13679 94.21852 assigned negative charge : -327.6889 centred at (gu) : 90.03503 93.44387 94.73286 start vw surface at 0.1200000 fill in re-entrant regions at 0.8500000 boundary points on vw surface= 179421 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20810 grid for indexing accessible points = 1.400000 m= 93867 mr = 126443 m= 39380 mr = 76326 m= 12193 mr = 31943 m= 2644 mr = 9286 m= 343 mr = 1906 m= 13 mr = 219 m= 0 mr = 1 time to grow re-entrant surface = 1.000000 no. cavity mid-points inaccessible to solvent = 400 time to turn everything in is 1.980000 number of dielectric boundary points 81737 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.160000 number of grid points assigned charge 16616 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) : 2.115731 object centre at (A) : 7.050000 5.970500 15.02200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6291547 2.0585144E-02 midg,1,midg; midg,igrid,midg 0.1525355 0.2792633 1,midg,midg; igrid,midg,midg 1.1734600E-02 0.3895221 gauss-seidel spectral radius is 0.9993010 estimated iterations to convergence 298 setup time was (sec) 2.370000 now iterating at: 14:01:48 rms-change max change #iterations 10.63049 377.6277 at 10iterations 6.216718 136.2883 at 20iterations 3.633994 65.73096 at 30iterations 2.124331 39.57969 at 40iterations 1.241598 21.71292 at 50iterations 0.7253797 14.22130 at 60iterations 0.4239273 7.902380 at 70iterations 0.2466931 4.329024 at 80iterations 0.1443773 2.392429 at 90iterations 8.4181540E-02 1.413656 at 100iterations 4.8973449E-02 0.8741226 at 110iterations 2.8557334E-02 0.4575281 at 120iterations 1.6646774E-02 0.2794304 at 130iterations 9.7067952E-03 0.1600666 at 140iterations 5.6525879E-03 9.3103409E-02 at 150iterations 3.2960938E-03 5.8549881E-02 at 160iterations 1.9213372E-03 3.1158447E-02 at 170iterations 1.1258185E-03 2.0465851E-02 at 180iterations finished qdiffx linear iterations at : 14:02:03 total time elapsed so far: 16.93000 # loops : 180 mean,max change (kT/e) : 1.1258185E-03 2.0465851E-02 energy calculations done at 16.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.12000 DelPhi exited at 14:02:04 17.117u 0.334s 0:17.97 97.0% 0+0k 0+0io 0pf+0w