Mon Oct 10 16:22:33 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 16:22:33 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4735 !!! WARNING: GLM 130 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5497561 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): -62.76200 -7.531000 ymin,ymax (A): -29.75900 34.73300 zmin,zma (A): -35.49700 29.25900 x,y,z range (A): 55.23100 64.49200 64.75600 scale (grids/A): 0.5497561 object centre (A): -35.14650 2.487001 -3.119001 number of atom coordinates read : 4735 total number of charged atoms : 4573 net assigned charge : 6.906020 assigned positive charge : 714.7919 centred at (gu) : 90.42257 90.11038 91.53237 assigned negative charge : -707.8901 centred at (gu) : 90.43060 90.06369 91.52156 start vw surface at 0.1600000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 9197 nv = 96 ne = 84 npr = 97469 no. pairs analyzed = 97469 no. exposed pairs = 5708 no. arc points = 38421 no. surface atoms = 1926 nbur = 2809 mkacc time = 0.2500000 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 = 1.568000 m= 379 mr = 5123 m= 0 mr = 17 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 7 time to turn everything in is 0.4900000 number of dielectric boundary points 4436 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3940 ## 507 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 12123 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5406791E-10 9.0757690E-10 midg,1,midg; midg,igrid,midg -7.3612408E-11 1.0868387E-09 1,midg,midg; igrid,midg,midg 5.3453558E-10 4.3801590E-10 gauss-seidel spectral radius is 0.9830642 estimated iterations to convergence 63 setup time was (sec) 0.7900000 now iterating at: 16:22:34 rms-change max change #iterations 9.9635027E-02 13.37929 at 10iterations 7.4416786E-03 0.8969040 at 20iterations 1.1567593E-03 0.2094307 at 30iterations 4.2385192E-04 6.8622589E-02 at 40iterations 1.7995940E-04 2.4482727E-02 at 50iterations finished qdiffx linear iterations at : 16:22:38 total time elapsed so far: 4.510000 # loops : 50 mean,max change (kT/e) : 1.7995940E-04 2.4482727E-02 energy calculations done at 4.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.670000 DelPhi exited at 16:22:38 4.679u 0.403s 0:05.39 94.0% 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 16:22:38 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4735 !!! WARNING: GLM 130 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.649268 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): -62.76200 -7.531000 ymin,ymax (A): -29.75900 34.73300 zmin,zma (A): -35.49700 29.25900 x,y,z range (A): 55.23100 64.49200 64.75600 scale (grids/A): 1.649268 object centre (A): -35.14650 2.487001 -3.119001 number of atom coordinates read : 4735 total number of charged atoms : 4573 net assigned charge : 6.906020 assigned positive charge : 714.7919 centred at (gu) : 91.26608 90.32993 94.59546 assigned negative charge : -707.8901 centred at (gu) : 91.29140 90.19057 94.56439 start vw surface at 0.1700000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 102953 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38421 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 32994 mr = 73583 m= 3452 mr = 22993 m= 108 mr = 1726 m= 0 mr = 8 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 652 time to turn everything in is 0.8300000 number of dielectric boundary points 41197 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 402 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 35084 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) : 0.5497561 object centre at (A) : -35.14650 2.487001 -3.119001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3175321E-03 1.6605306E-02 midg,1,midg; midg,igrid,midg 1.7451596E-02 1.5750980E-02 1,midg,midg; igrid,midg,midg 5.5115512E-03 3.7164369E-03 gauss-seidel spectral radius is 0.9983891 estimated iterations to convergence 198 setup time was (sec) 1.150000 now iterating at: 16:22:40 rms-change max change #iterations 4.421148 204.3866 at 10iterations 1.942835 62.97303 at 20iterations 0.8515751 25.07369 at 30iterations 0.3741904 11.86715 at 40iterations 0.1644113 4.865533 at 50iterations 7.2221301E-02 2.149169 at 60iterations 3.1951237E-02 0.9725609 at 70iterations 1.4168771E-02 0.4376450 at 80iterations 6.3568605E-03 0.1921387 at 90iterations 2.9671227E-03 9.4234467E-02 at 100iterations 1.4688794E-03 4.7710419E-02 at 110iterations 8.2421559E-04 2.3845673E-02 at 120iterations finished qdiffx linear iterations at : 16:22:50 total time elapsed so far: 10.84000 # loops : 120 mean,max change (kT/e) : 8.2421559E-04 2.3845673E-02 energy calculations done at 10.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.01000 DelPhi exited at 16:22:50 11.014u 0.445s 0:11.72 97.6% 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 16:22:50 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4735 !!! WARNING: GLM 130 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.473902 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): -62.76200 -7.531000 ymin,ymax (A): -29.75900 34.73300 zmin,zma (A): -35.49700 29.25900 x,y,z range (A): 55.23100 64.49200 64.75600 scale (grids/A): 2.473902 object centre (A): -35.14650 2.487001 -3.119001 number of atom coordinates read : 4735 total number of charged atoms : 4573 net assigned charge : 6.906020 assigned positive charge : 714.7919 centred at (gu) : 91.89878 90.49450 96.89276 assigned negative charge : -707.8901 centred at (gu) : 91.93694 90.28579 96.84653 start vw surface at 0.1800000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 239680 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38421 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 114012 mr = 179659 m= 32758 mr = 91363 m= 5444 mr = 24563 m= 443 mr = 3602 m= 9 mr = 232 m= 0 mr = 0 time to grow re-entrant surface = 1.300000 no. cavity mid-points inaccessible to solvent = 2088 time to turn everything in is 2.100000 number of dielectric boundary points 92927 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 2.260000 number of grid points assigned charge 36542 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) : 1.649268 object centre at (A) : -35.14650 2.487001 -3.119001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.8762237E-02 0.4593163 midg,1,midg; midg,igrid,midg 0.3673043 0.1646663 1,midg,midg; igrid,midg,midg 0.1040036 7.7370480E-02 gauss-seidel spectral radius is 0.9992349 estimated iterations to convergence 285 setup time was (sec) 2.460000 now iterating at: 16:22:53 rms-change max change #iterations 11.40684 413.6376 at 10iterations 6.707680 173.8262 at 20iterations 3.915290 81.94601 at 30iterations 2.281275 45.36959 at 40iterations 1.319977 25.04926 at 50iterations 0.7631984 15.31202 at 60iterations 0.4395540 7.993536 at 70iterations 0.2528709 4.897428 at 80iterations 0.1452449 2.363210 at 90iterations 8.3346076E-02 1.453868 at 100iterations 4.7771957E-02 0.7807968 at 110iterations 2.7347168E-02 0.4695892 at 120iterations 1.5665922E-02 0.2530003 at 130iterations 8.9820921E-03 0.1563797 at 140iterations 5.1481654E-03 9.0487480E-02 at 150iterations 2.9738660E-03 5.0783634E-02 at 160iterations 1.7266396E-03 2.9285431E-02 at 170iterations 1.0244579E-03 1.9035339E-02 at 180iterations finished qdiffx linear iterations at : 16:23:10 total time elapsed so far: 19.38000 # loops : 180 mean,max change (kT/e) : 1.0244579E-03 1.9035339E-02 energy calculations done at 19.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.55000 DelPhi exited at 16:23:10 19.552u 0.462s 0:20.29 98.6% 0+0k 0+0io 0pf+0w