Tue Oct 11 02:37:00 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 02:37:00 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2777 !!! WARNING: GLM 47 has a net charge of -0.0940 !!! WARNING: FMN 398 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: 0.6686324 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): 20.54600 67.71900 ymin,ymax (A): 14.47000 67.71301 zmin,zma (A): -17.33000 30.31000 x,y,z range (A): 47.17300 53.24300 47.64000 scale (grids/A): 0.6686324 object centre (A): 44.13250 41.09150 6.490000 number of atom coordinates read : 2777 total number of charged atoms : 2638 net assigned charge : 5.406027 assigned positive charge : 427.1582 centred at (gu) : 90.66564 90.37840 90.23170 assigned negative charge : -421.7534 centred at (gu) : 90.47355 90.54825 90.27964 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 8324 nv = 96 ne = 84 npr = 57107 no. pairs analyzed = 57107 no. exposed pairs = 3449 no. arc points = 23714 no. surface atoms = 1148 nbur = 1629 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 440 mr = 4706 m= 5 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 45 time to turn everything in is 0.2100000 number of dielectric boundary points 4007 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2293 ## 198 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9789 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8624518E-08 4.5227138E-09 midg,1,midg; midg,igrid,midg 5.7232732E-08 -3.1501649E-08 1,midg,midg; igrid,midg,midg -3.0487545E-08 7.7620697E-08 gauss-seidel spectral radius is 0.9884204 estimated iterations to convergence 76 setup time was (sec) 0.4000000 now iterating at: 02:37:01 rms-change max change #iterations 0.1856997 23.68580 at 10iterations 2.0846099E-02 2.744568 at 20iterations 2.5641024E-03 0.3149033 at 30iterations 4.1645372E-04 6.9107056E-02 at 40iterations 9.2846960E-05 1.6677856E-02 at 50iterations finished qdiffx linear iterations at : 02:37:04 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 9.2846960E-05 1.6677856E-02 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 02:37:04 3.416u 0.186s 0:04.11 87.3% 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 02:37:04 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 # of charge parameter records: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2777 !!! WARNING: GLM 47 has a net charge of -0.0940 !!! WARNING: FMN 398 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: 2.005897 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): 20.54600 67.71900 ymin,ymax (A): 14.47000 67.71301 zmin,zma (A): -17.33000 30.31000 x,y,z range (A): 47.17300 53.24300 47.64000 scale (grids/A): 2.005897 object centre (A): 44.13250 41.09150 6.490000 number of atom coordinates read : 2777 total number of charged atoms : 2638 net assigned charge : 5.406027 assigned positive charge : 427.1582 centred at (gu) : 91.99645 91.13452 90.69421 assigned negative charge : -421.7534 centred at (gu) : 91.42028 91.64433 90.83883 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 90323 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23714 grid for indexing accessible points = 1.400000 m= 33193 mr = 63926 m= 5536 mr = 24837 m= 419 mr = 3531 m= 5 mr = 166 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 2412 time to turn everything in is 0.4300000 number of dielectric boundary points 37016 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 126 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 20868 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) : 0.6686324 object centre at (A) : 44.13250 41.09150 6.490000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7198272E-02 -2.9031696E-02 midg,1,midg; midg,igrid,midg 8.0414377E-02 -2.4610357E-02 1,midg,midg; igrid,midg,midg -1.9735724E-02 7.1639821E-02 gauss-seidel spectral radius is 0.9987835 estimated iterations to convergence 227 setup time was (sec) 0.6400000 now iterating at: 02:37:05 rms-change max change #iterations 4.930188 241.5233 at 10iterations 2.404212 81.25000 at 20iterations 1.175323 37.09080 at 30iterations 0.5723664 17.34409 at 40iterations 0.2802112 8.862957 at 50iterations 0.1372110 3.959117 at 60iterations 6.7121692E-02 1.990829 at 70iterations 3.3067938E-02 0.8679600 at 80iterations 1.6362133E-02 0.5450916 at 90iterations 8.2038725E-03 0.2311993 at 100iterations 4.2412942E-03 0.1392937 at 110iterations 2.2737312E-03 8.5617065E-02 at 120iterations finished qdiffx linear iterations at : 02:37:12 total time elapsed so far: 7.830000 # loops : 120 mean,max change (kT/e) : 2.2737312E-03 8.5617065E-02 energy calculations done at 7.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.950000 DelPhi exited at 02:37:13 7.957u 0.213s 0:08.87 91.9% 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 02:37:13 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: 288 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2777 !!! WARNING: GLM 47 has a net charge of -0.0940 !!! WARNING: FMN 398 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: 3.008846 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): 20.54600 67.71900 ymin,ymax (A): 14.47000 67.71301 zmin,zma (A): -17.33000 30.31000 x,y,z range (A): 47.17300 53.24300 47.64000 scale (grids/A): 3.008846 object centre (A): 44.13250 41.09150 6.490000 number of atom coordinates read : 2777 total number of charged atoms : 2638 net assigned charge : 5.406027 assigned positive charge : 427.1582 centred at (gu) : 92.99438 91.70161 91.04111 assigned negative charge : -421.7534 centred at (gu) : 92.13036 92.46644 91.25810 start vw surface at 0.1000000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 208555 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23714 grid for indexing accessible points = 1.400000 m= 106846 mr = 154183 m= 39813 mr = 88243 m= 10277 mr = 32372 m= 1688 mr = 7858 m= 122 mr = 1137 m= 3 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 8042 time to turn everything in is 1.150000 number of dielectric boundary points 83454 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.240000 number of grid points assigned charge 21104 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) : 2.005897 object centre at (A) : 44.13250 41.09150 6.490000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2231114 -0.3377478 midg,1,midg; midg,igrid,midg 1.016031 -0.4693929 1,midg,midg; igrid,midg,midg -0.2221406 0.6813731 gauss-seidel spectral radius is 0.9992967 estimated iterations to convergence 297 setup time was (sec) 1.390000 now iterating at: 02:37:15 rms-change max change #iterations 11.27482 361.3845 at 10iterations 6.657150 137.9445 at 20iterations 3.928825 70.80544 at 30iterations 2.306612 47.21178 at 40iterations 1.358057 22.62708 at 50iterations 0.7982855 12.77589 at 60iterations 0.4666037 7.851105 at 70iterations 0.2733404 4.342583 at 80iterations 0.1599486 2.516782 at 90iterations 9.3552284E-02 1.523215 at 100iterations 5.4925688E-02 0.8838863 at 110iterations 3.2134965E-02 0.5534534 at 120iterations 1.8894399E-02 0.3628845 at 130iterations 1.1188086E-02 0.2035522 at 140iterations 6.7216321E-03 0.1307068 at 150iterations 4.1295718E-03 9.2845917E-02 at 160iterations 2.6432378E-03 5.8120728E-02 at 170iterations 1.7848025E-03 3.8650513E-02 at 180iterations finished qdiffx linear iterations at : 02:37:26 total time elapsed so far: 12.90000 # loops : 180 mean,max change (kT/e) : 1.7848025E-03 3.8650513E-02 energy calculations done at 12.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.05000 DelPhi exited at 02:37:27 13.050u 0.186s 0:13.57 97.4% 0+0k 0+0io 0pf+0w