Wed Nov 9 08:20:38 PST 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 Wed Nov 9 2011 at 08:20:38 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 ! Automatically converted by prot2crg.py # of charge parameter records: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3686 !!! WARNING: HEM 900 has a net charge of -2.0000 !!! WARNING: ZN 951 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5559980 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): -30.10400 33.92500 ymin,ymax (A): -31.44200 31.33500 zmin,zma (A): 29.24300 86.38400 x,y,z range (A): 64.02901 62.77700 57.14100 scale (grids/A): 0.5559980 object centre (A): 1.910501 -5.3500175E-02 57.81350 number of atom coordinates read : 3686 total number of charged atoms : 3534 net assigned charge : -6.599985 assigned positive charge : 557.4215 centred at (gu) : 90.00468 91.65693 91.20033 assigned negative charge : -564.0234 centred at (gu) : 90.08995 91.72526 91.14634 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7315 nv = 96 ne = 84 npr = 75393 no. pairs analyzed = 75393 no. exposed pairs = 4731 no. arc points = 33061 no. surface atoms = 1570 nbur = 2116 mkacc time = 0.1500000 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 = 1.540000 m= 285 mr = 3736 m= 1 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 3843 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3310 ## 376 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 9587 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -9.3863617E-10 8.7351522E-11 midg,1,midg; midg,igrid,midg 1.4387989E-10 -2.1457569E-09 1,midg,midg; igrid,midg,midg 4.2849679E-10 -1.6402396E-09 gauss-seidel spectral radius is 0.9833693 estimated iterations to convergence 64 setup time was (sec) 0.5000000 now iterating at: 08:20:39 rms-change max change #iterations 8.9046754E-02 13.51138 at 10iterations 6.3203834E-03 1.131198 at 20iterations 5.3799147E-04 8.9622498E-02 at 30iterations 8.8203698E-05 1.3593674E-02 at 40iterations 2.3177616E-05 3.8080215E-03 at 50iterations finished qdiffx linear iterations at : 08:20:42 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 2.3177616E-05 3.8080215E-03 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 08:20:43 3.609u 0.189s 0:04.74 79.7% 0+0k 0+46216io 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 Wed Nov 9 2011 at 08:20:43 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 ! Automatically converted by prot2crg.py # of charge parameter records: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3686 !!! WARNING: HEM 900 has a net charge of -2.0000 !!! WARNING: ZN 951 has a net charge of 1.4000 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: 1.667994 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): -30.10400 33.92500 ymin,ymax (A): -31.44200 31.33500 zmin,zma (A): 29.24300 86.38400 x,y,z range (A): 64.02901 62.77700 57.14100 scale (grids/A): 1.667994 object centre (A): 1.910501 -5.3500175E-02 57.81350 number of atom coordinates read : 3686 total number of charged atoms : 3534 net assigned charge : -6.599985 assigned positive charge : 557.4215 centred at (gu) : 90.01292 94.96970 93.59999 assigned negative charge : -564.0234 centred at (gu) : 90.26952 95.17494 93.43865 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 80626 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33061 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 24708 mr = 54659 m= 2682 mr = 16720 m= 93 mr = 1308 m= 0 mr = 7 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 35415 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 348 iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 27271 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) : 0.5559980 object centre at (A) : 1.910501 -5.3500175E-02 57.81350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0801590E-02 -7.8306952E-03 midg,1,midg; midg,igrid,midg -1.0083062E-02 -2.2757852E-02 1,midg,midg; igrid,midg,midg 9.3868207E-03 -9.8464638E-03 gauss-seidel spectral radius is 0.9983307 estimated iterations to convergence 194 setup time was (sec) 0.7000000 now iterating at: 08:20:56 rms-change max change #iterations 3.990046 154.8507 at 10iterations 1.716839 66.28206 at 20iterations 0.7429560 25.02949 at 30iterations 0.3195235 11.00608 at 40iterations 0.1379093 4.472666 at 50iterations 5.9854623E-02 1.872837 at 60iterations 2.5837144E-02 0.9159794 at 70iterations 1.1183560E-02 0.3460813 at 80iterations 4.8446939E-03 0.1608810 at 90iterations 2.1108787E-03 6.6587448E-02 at 100iterations 9.2283724E-04 3.0216217E-02 at 110iterations 4.0831580E-04 1.2573242E-02 at 120iterations finished qdiffx linear iterations at : 08:21:03 total time elapsed so far: 7.970000 # loops : 120 mean,max change (kT/e) : 4.0831580E-04 1.2573242E-02 energy calculations done at 7.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.120000 DelPhi exited at 08:21:04 8.124u 0.218s 0:21.42 38.8% 0+0k 0+45416io 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 Wed Nov 9 2011 at 08:21:04 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 ! Automatically converted by prot2crg.py # of charge parameter records: 327 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3686 !!! WARNING: HEM 900 has a net charge of -2.0000 !!! WARNING: ZN 951 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.501991 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): -30.10400 33.92500 ymin,ymax (A): -31.44200 31.33500 zmin,zma (A): 29.24300 86.38400 x,y,z range (A): 64.02901 62.77700 57.14100 scale (grids/A): 2.501991 object centre (A): 1.910501 -5.3500175E-02 57.81350 number of atom coordinates read : 3686 total number of charged atoms : 3534 net assigned charge : -6.599985 assigned positive charge : 557.4215 centred at (gu) : 90.01920 97.45422 95.39960 assigned negative charge : -564.0234 centred at (gu) : 90.40403 97.76244 95.15788 start vw surface at 0.1300000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 187253 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33061 grid for indexing accessible points = 1.400000 m= 85912 mr = 133812 m= 24033 mr = 67483 m= 4189 mr = 17708 m= 387 mr = 2730 m= 5 mr = 178 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.240000 number of dielectric boundary points 79868 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 28250 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) : 1.667994 object centre at (A) : 1.910501 -5.3500175E-02 57.81350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1303763 -3.7116684E-02 midg,1,midg; midg,igrid,midg -0.3306434 -0.3277571 1,midg,midg; igrid,midg,midg 0.1165221 -3.8492192E-02 gauss-seidel spectral radius is 0.9991957 estimated iterations to convergence 278 setup time was (sec) 1.470000 now iterating at: 08:21:06 rms-change max change #iterations 10.12282 325.8599 at 10iterations 5.809697 146.3440 at 20iterations 3.304887 69.87653 at 30iterations 1.881478 40.83917 at 40iterations 1.066701 22.49886 at 50iterations 0.6027510 11.70239 at 60iterations 0.3403293 7.803543 at 70iterations 0.1916592 4.267628 at 80iterations 0.1084691 2.146892 at 90iterations 6.0978916E-02 1.272877 at 100iterations 3.4307770E-02 0.6511154 at 110iterations 1.9296059E-02 0.3794441 at 120iterations 1.0842592E-02 0.2120295 at 130iterations 6.0967417E-03 0.1146193 at 140iterations 3.4142435E-03 6.3335419E-02 at 150iterations 1.9186572E-03 3.5572529E-02 at 160iterations 1.0773760E-03 2.0622253E-02 at 170iterations 6.0551474E-04 1.1157990E-02 at 180iterations finished qdiffx linear iterations at : 08:21:18 total time elapsed so far: 13.00000 # loops : 180 mean,max change (kT/e) : 6.0551474E-04 1.1157990E-02 energy calculations done at 13.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.15000 DelPhi exited at 08:21:18 13.159u 0.218s 0:14.19 94.1% 0+0k 0+45408io 0pf+0w