Mon Oct 10 19:32:26 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 19:32:26 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 = 2702 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5276576 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): -57.20700 10.26100 ymin,ymax (A): -45.27700 10.33400 zmin,zma (A): -12.02800 35.40300 x,y,z range (A): 67.46799 55.61100 47.43100 scale (grids/A): 0.5276576 object centre (A): -23.47300 -17.47150 11.68750 number of atom coordinates read : 2702 total number of charged atoms : 2568 net assigned charge : 12.50002 assigned positive charge : 398.6766 centred at (gu) : 89.64136 89.76010 90.25867 assigned negative charge : -386.1775 centred at (gu) : 89.71498 89.84859 90.21196 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 4930 nv = 96 ne = 84 npr = 53604 no. pairs analyzed = 53604 no. exposed pairs = 3606 no. arc points = 25374 no. surface atoms = 1214 nbur = 1488 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 217 mr = 2397 m= 2 mr = 6 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 0.2900000 number of dielectric boundary points 2746 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2613 ## 371 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 6502 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2139832E-10 5.3500004E-10 midg,1,midg; midg,igrid,midg 6.5672606E-10 1.0879775E-10 1,midg,midg; igrid,midg,midg 6.3135402E-10 1.4531829E-10 gauss-seidel spectral radius is 0.9814818 estimated iterations to convergence 61 setup time was (sec) 0.5200000 now iterating at: 19:32:27 rms-change max change #iterations 5.5970225E-02 10.46605 at 10iterations 3.3502048E-03 0.6228199 at 20iterations 2.0821505E-04 3.6937714E-02 at 30iterations 1.2925891E-05 2.6187897E-03 at 40iterations 8.3348442E-07 1.4138222E-04 at 50iterations finished qdiffx linear iterations at : 19:32:29 total time elapsed so far: 3.120000 # loops : 50 mean,max change (kT/e) : 8.3348442E-07 1.4138222E-04 energy calculations done at 3.120000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 19:32:30 3.302u 0.173s 0:04.16 83.4% 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 19:32:30 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 = 2702 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.582973 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): -57.20700 10.26100 ymin,ymax (A): -45.27700 10.33400 zmin,zma (A): -12.02800 35.40300 x,y,z range (A): 67.46799 55.61100 47.43100 scale (grids/A): 1.582973 object centre (A): -23.47300 -17.47150 11.68750 number of atom coordinates read : 2702 total number of charged atoms : 2568 net assigned charge : 12.50002 assigned positive charge : 398.6766 centred at (gu) : 88.92375 89.27980 90.77515 assigned negative charge : -386.1775 centred at (gu) : 89.14470 89.54546 90.63570 start vw surface at 0.1700000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 54572 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25374 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 16225 mr = 35647 m= 1559 mr = 10603 m= 46 mr = 665 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 680 time to turn everything in is 0.4400000 number of dielectric boundary points 25487 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 343 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 19487 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) : 0.5276576 object centre at (A) : -23.47300 -17.47150 11.68750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.7562133E-03 1.5020896E-02 midg,1,midg; midg,igrid,midg 7.2860196E-03 -3.5022059E-03 1,midg,midg; igrid,midg,midg 2.9486911E-03 -8.4488466E-03 gauss-seidel spectral radius is 0.9980409 estimated iterations to convergence 180 setup time was (sec) 0.7300000 now iterating at: 19:32:31 rms-change max change #iterations 2.861728 153.7057 at 10iterations 1.152261 49.42268 at 20iterations 0.4638714 19.10709 at 30iterations 0.1862772 8.038696 at 40iterations 7.4998461E-02 3.372252 at 50iterations 3.0312305E-02 1.142326 at 60iterations 1.2163376E-02 0.5266800 at 70iterations 4.9061673E-03 0.1879883 at 80iterations 1.9752635E-03 7.8628540E-02 at 90iterations 7.9578161E-04 3.2809258E-02 at 100iterations 3.1979370E-04 1.2362480E-02 at 110iterations 1.2957249E-04 5.5818558E-03 at 120iterations finished qdiffx linear iterations at : 19:32:38 total time elapsed so far: 7.230000 # loops : 120 mean,max change (kT/e) : 1.2957249E-04 5.5818558E-03 energy calculations done at 7.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.430000 DelPhi exited at 19:32:39 7.434u 0.236s 0:08.98 85.3% 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 19:32:39 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 = 2702 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.374459 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): -57.20700 10.26100 ymin,ymax (A): -45.27700 10.33400 zmin,zma (A): -12.02800 35.40300 x,y,z range (A): 67.46799 55.61100 47.43100 scale (grids/A): 2.374459 object centre (A): -23.47300 -17.47150 11.68750 number of atom coordinates read : 2702 total number of charged atoms : 2568 net assigned charge : 12.50002 assigned positive charge : 398.6766 centred at (gu) : 88.38536 88.91968 91.16267 assigned negative charge : -386.1775 centred at (gu) : 88.71690 89.31822 90.95340 start vw surface at 0.1600000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 126721 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25374 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 56635 mr = 87497 m= 15217 mr = 43810 m= 2355 mr = 10761 m= 142 mr = 1346 m= 2 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 2285 time to turn everything in is 0.9700000 number of dielectric boundary points 57598 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 31 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 20506 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) : 1.582973 object centre at (A) : -23.47300 -17.47150 11.68750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.0506269E-02 0.2442897 midg,1,midg; midg,igrid,midg 0.1053322 -5.1431831E-02 1,midg,midg; igrid,midg,midg 2.9747525E-02 -0.2490945 gauss-seidel spectral radius is 0.9990875 estimated iterations to convergence 262 setup time was (sec) 1.290000 now iterating at: 19:32:41 rms-change max change #iterations 7.649691 279.6641 at 10iterations 4.225631 136.1443 at 20iterations 2.319821 71.06886 at 30iterations 1.270027 33.25771 at 40iterations 0.6922743 17.67749 at 50iterations 0.3764848 8.712767 at 60iterations 0.2038996 5.706988 at 70iterations 0.1106147 2.798209 at 80iterations 5.9759453E-02 1.460969 at 90iterations 3.2358710E-02 0.7468834 at 100iterations 1.7429730E-02 0.3857566 at 110iterations 9.4475485E-03 0.2255225 at 120iterations 5.0953506E-03 0.1158466 at 130iterations 2.7506719E-03 6.3735962E-02 at 140iterations 1.4799335E-03 3.2658577E-02 at 150iterations 8.0158422E-04 1.9901276E-02 at 160iterations 4.3170908E-04 1.0892391E-02 at 170iterations 2.3280070E-04 5.5336952E-03 at 180iterations finished qdiffx linear iterations at : 19:32:51 total time elapsed so far: 11.57000 # loops : 180 mean,max change (kT/e) : 2.3280070E-04 5.5336952E-03 energy calculations done at 11.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.75000 DelPhi exited at 19:32:52 11.756u 0.289s 0:12.59 95.5% 0+0k 0+0io 0pf+0w