Tue Oct 11 08:34:32 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 Tue Oct 11 2011 at 08:34:32 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2097 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 0.7047551 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): -19.70100 27.22300 ymin,ymax (A): -12.46100 28.76500 zmin,zma (A): -2.041000 48.47300 x,y,z range (A): 46.92400 41.22600 50.51400 scale (grids/A): 0.7047551 object centre (A): 3.761000 8.152000 23.21600 number of atom coordinates read : 2097 total number of charged atoms : 1961 net assigned charge : 5.470011 assigned positive charge : 319.8660 centred at (gu) : 88.94962 89.72922 90.09219 assigned negative charge : -314.3961 centred at (gu) : 88.82726 89.76109 90.14490 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7096 nv = 96 ne = 84 npr = 42198 no. pairs analyzed = 42198 no. exposed pairs = 2543 no. arc points = 17310 no. surface atoms = 867 nbur = 1230 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 465 mr = 4122 m= 3 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.3200000 number of dielectric boundary points 3355 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1574 ## 140 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7772 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.7338448E-08 1.9439543E-08 midg,1,midg; midg,igrid,midg 6.2004375E-08 2.7585326E-08 1,midg,midg; igrid,midg,midg -1.8098307E-08 8.2072440E-08 gauss-seidel spectral radius is 0.9895059 estimated iterations to convergence 79 setup time was (sec) 0.6000000 now iterating at: 08:34:33 rms-change max change #iterations 0.2005498 27.64714 at 10iterations 2.5107229E-02 3.413254 at 20iterations 3.4870435E-03 0.4465876 at 30iterations 6.4438110E-04 7.8874588E-02 at 40iterations 1.7491021E-04 2.4301529E-02 at 50iterations finished qdiffx linear iterations at : 08:34:36 total time elapsed so far: 3.770000 # loops : 50 mean,max change (kT/e) : 1.7491021E-04 2.4301529E-02 energy calculations done at 3.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.000000 DelPhi exited at 08:34:37 4.002u 0.189s 0:04.48 93.3% 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 Tue Oct 11 2011 at 08:34:37 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2097 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 2.114265 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): -19.70100 27.22300 ymin,ymax (A): -12.46100 28.76500 zmin,zma (A): -2.041000 48.47300 x,y,z range (A): 46.92400 41.22600 50.51400 scale (grids/A): 2.114265 object centre (A): 3.761000 8.152000 23.21600 number of atom coordinates read : 2097 total number of charged atoms : 1961 net assigned charge : 5.470011 assigned positive charge : 319.8660 centred at (gu) : 86.84890 89.18800 90.27685 assigned negative charge : -314.3961 centred at (gu) : 86.48181 89.28343 90.43483 start vw surface at 0.2000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 75133 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17310 grid for indexing accessible points = 1.400000 m= 30484 mr = 53784 m= 6003 mr = 23275 m= 536 mr = 4165 m= 12 mr = 298 m= 0 mr = 2 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7300000 number of dielectric boundary points 30644 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 74 iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 15546 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) : 0.7047551 object centre at (A) : 3.761000 8.152000 23.21600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3177290E-02 5.9530791E-02 midg,1,midg; midg,igrid,midg 2.5980270E-02 1.2383029E-03 1,midg,midg; igrid,midg,midg 1.1782921E-02 3.2965865E-02 gauss-seidel spectral radius is 0.9988236 estimated iterations to convergence 231 setup time was (sec) 1.080000 now iterating at: 08:34:38 rms-change max change #iterations 4.604731 234.7857 at 10iterations 2.267017 71.89863 at 20iterations 1.124347 33.50839 at 30iterations 0.5546458 17.07829 at 40iterations 0.2752496 8.794198 at 50iterations 0.1363260 4.328829 at 60iterations 6.7819133E-02 2.095590 at 70iterations 3.3661827E-02 1.039478 at 80iterations 1.6835317E-02 0.5569162 at 90iterations 8.4732519E-03 0.2615986 at 100iterations 4.3213582E-03 0.1305542 at 110iterations 2.2515226E-03 6.8036079E-02 at 120iterations finished qdiffx linear iterations at : 08:34:46 total time elapsed so far: 8.740000 # loops : 120 mean,max change (kT/e) : 2.2515226E-03 6.8036079E-02 energy calculations done at 8.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.970000 DelPhi exited at 08:34:46 8.971u 0.173s 0:09.79 93.3% 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 Tue Oct 11 2011 at 08:34:46 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: 291 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2097 !!! WARNING: HIR 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 !!! WARNING: SEP 195 has a net charge of -0.4750 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: 3.171398 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): -19.70100 27.22300 ymin,ymax (A): -12.46100 28.76500 zmin,zma (A): -2.041000 48.47300 x,y,z range (A): 46.92400 41.22600 50.51400 scale (grids/A): 3.171398 object centre (A): 3.761000 8.152000 23.21600 number of atom coordinates read : 2097 total number of charged atoms : 1961 net assigned charge : 5.470011 assigned positive charge : 319.8660 centred at (gu) : 85.27325 88.78192 90.41512 assigned negative charge : -314.3961 centred at (gu) : 84.72275 88.92516 90.65238 start vw surface at 0.1800000 fill in re-entrant regions at 1.000000 boundary points on vw surface= 172931 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17310 grid for indexing accessible points = 1.400000 m= 94825 mr = 128717 m= 39090 mr = 79560 m= 11556 mr = 32539 m= 2431 mr = 9125 m= 237 mr = 1773 m= 5 mr = 146 m= 0 mr = 4 time to grow re-entrant surface = 1.130000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.260000 number of dielectric boundary points 69211 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.420000 number of grid points assigned charge 15684 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) : 2.114265 object centre at (A) : 3.761000 8.152000 23.21600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2215449 1.311176 midg,1,midg; midg,igrid,midg 0.2016131 -1.4493381E-02 1,midg,midg; igrid,midg,midg 0.2581626 0.2979849 gauss-seidel spectral radius is 0.9992923 estimated iterations to convergence 297 setup time was (sec) 2.630000 now iterating at: 08:34:49 rms-change max change #iterations 10.26343 352.0519 at 10iterations 6.066570 125.6027 at 20iterations 3.566009 75.37399 at 30iterations 2.103844 42.14357 at 40iterations 1.234879 24.50629 at 50iterations 0.7244840 13.64648 at 60iterations 0.4244439 7.610439 at 70iterations 0.2484968 4.831085 at 80iterations 0.1453297 2.517723 at 90iterations 8.4995404E-02 1.559525 at 100iterations 5.0005257E-02 0.9234486 at 110iterations 2.9446654E-02 0.5780125 at 120iterations 1.7451301E-02 0.2968483 at 130iterations 1.0543711E-02 0.1866608 at 140iterations 6.5198434E-03 0.1290464 at 150iterations 4.1924659E-03 8.4955215E-02 at 160iterations 2.8321526E-03 5.2074432E-02 at 170iterations 2.0296192E-03 3.6148071E-02 at 180iterations finished qdiffx linear iterations at : 08:35:01 total time elapsed so far: 14.85000 # loops : 180 mean,max change (kT/e) : 2.0296192E-03 3.6148071E-02 energy calculations done at 14.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.08000 DelPhi exited at 08:35:02 15.082u 0.188s 0:15.59 97.8% 0+0k 0+0io 0pf+0w