Mon Oct 10 11:34:36 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 11:34:36 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2139 !!! WARNING: ASL 51 has a net charge of -0.1000 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: 0.7154341 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): -22.09600 23.23700 ymin,ymax (A): 7.814000 49.51800 zmin,zma (A): -24.32600 25.43400 x,y,z range (A): 45.33300 41.70400 49.76000 scale (grids/A): 0.7154341 object centre (A): 0.5705004 28.66600 0.5539999 number of atom coordinates read : 2139 total number of charged atoms : 1999 net assigned charge : -6.099979 assigned positive charge : 323.0838 centred at (gu) : 89.31691 90.99069 90.98029 assigned negative charge : -329.1840 centred at (gu) : 89.46561 90.87012 90.81104 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7351 nv = 96 ne = 84 npr = 44469 no. pairs analyzed = 44469 no. exposed pairs = 2679 no. arc points = 19020 no. surface atoms = 896 nbur = 1243 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 445 mr = 4015 m= 5 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 131 time to turn everything in is 0.3100000 number of dielectric boundary points 3724 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1592 ## 120 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 8070 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4190124E-07 4.8349399E-08 midg,1,midg; midg,igrid,midg -1.1599676E-07 1.2654394E-08 1,midg,midg; igrid,midg,midg 3.1134828E-08 -1.3869334E-07 gauss-seidel spectral radius is 0.9898254 estimated iterations to convergence 81 setup time was (sec) 0.7900000 now iterating at: 11:34:38 rms-change max change #iterations 0.2197254 34.60166 at 10iterations 2.7188340E-02 3.947575 at 20iterations 3.4333610E-03 0.4437180 at 30iterations 4.2687761E-04 5.7312012E-02 at 40iterations 5.4536958E-05 6.8922043E-03 at 50iterations finished qdiffx linear iterations at : 11:34:45 total time elapsed so far: 7.860000 # loops : 50 mean,max change (kT/e) : 5.4536958E-05 6.8922043E-03 energy calculations done at 7.860000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.030000 DelPhi exited at 11:34:45 8.036u 0.731s 0:09.05 96.7% 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 11:34:45 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2139 !!! WARNING: ASL 51 has a net charge of -0.1000 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: 2.146302 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): -22.09600 23.23700 ymin,ymax (A): 7.814000 49.51800 zmin,zma (A): -24.32600 25.43400 x,y,z range (A): 45.33300 41.70400 49.76000 scale (grids/A): 2.146302 object centre (A): 0.5705004 28.66600 0.5539999 number of atom coordinates read : 2139 total number of charged atoms : 1999 net assigned charge : -6.099979 assigned positive charge : 323.0838 centred at (gu) : 87.95083 92.97218 92.94057 assigned negative charge : -329.1840 centred at (gu) : 88.39688 92.61049 92.43300 start vw surface at 0.1200000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 77707 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19020 grid for indexing accessible points = 1.400000 m= 29585 mr = 53169 m= 5881 mr = 22163 m= 545 mr = 3945 m= 14 mr = 250 m= 0 mr = 2 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 3759 time to turn everything in is 0.7700000 number of dielectric boundary points 34203 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 47 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 15893 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) : 0.7154341 object centre at (A) : 0.5705004 28.66600 0.5539999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.7441688E-02 -3.4581643E-02 midg,1,midg; midg,igrid,midg -3.4736965E-02 -2.8328314E-02 1,midg,midg; igrid,midg,midg 2.5410181E-02 -1.1733128E-02 gauss-seidel spectral radius is 0.9988636 estimated iterations to convergence 235 setup time was (sec) 1.330000 now iterating at: 11:34:47 rms-change max change #iterations 4.873368 205.6111 at 10iterations 2.424294 97.33629 at 20iterations 1.212718 36.84695 at 30iterations 0.6033216 17.78176 at 40iterations 0.3012349 9.295124 at 50iterations 0.1512515 4.926304 at 60iterations 7.5340822E-02 2.105896 at 70iterations 3.7796509E-02 1.139858 at 80iterations 1.8886175E-02 0.6138415 at 90iterations 9.4539048E-03 0.2891006 at 100iterations 4.7345650E-03 0.1384430 at 110iterations 2.3675768E-03 6.9370627E-02 at 120iterations finished qdiffx linear iterations at : 11:35:03 total time elapsed so far: 16.69000 # loops : 120 mean,max change (kT/e) : 2.3675768E-03 6.9370627E-02 energy calculations done at 16.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.87000 DelPhi exited at 11:35:03 16.879u 0.826s 0:18.01 98.2% 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 11:35:03 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2139 !!! WARNING: ASL 51 has a net charge of -0.1000 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: 3.219453 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): -22.09600 23.23700 ymin,ymax (A): 7.814000 49.51800 zmin,zma (A): -24.32600 25.43400 x,y,z range (A): 45.33300 41.70400 49.76000 scale (grids/A): 3.219453 object centre (A): 0.5705004 28.66600 0.5539999 number of atom coordinates read : 2139 total number of charged atoms : 1999 net assigned charge : -6.099979 assigned positive charge : 323.0838 centred at (gu) : 86.92619 94.45830 94.41080 assigned negative charge : -329.1840 centred at (gu) : 87.59537 93.91579 93.64955 start vw surface at 0.1200000 fill in re-entrant regions at 0.9200000 boundary points on vw surface= 178981 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19020 grid for indexing accessible points = 1.400000 m= 92214 mr = 128417 m= 37423 mr = 75733 m= 11108 mr = 30720 m= 2238 mr = 8590 m= 263 mr = 1604 m= 5 mr = 142 m= 0 mr = 0 time to grow re-entrant surface = 1.210000 no. cavity mid-points inaccessible to solvent = 12838 time to turn everything in is 2.320000 number of dielectric boundary points 77026 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.580000 number of grid points assigned charge 15992 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) : 2.146302 object centre at (A) : 0.5705004 28.66600 0.5539999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.8067454 -0.2528751 midg,1,midg; midg,igrid,midg -0.2294247 -0.2772574 1,midg,midg; igrid,midg,midg 0.1469940 -6.0573515E-02 gauss-seidel spectral radius is 0.9993030 estimated iterations to convergence 299 setup time was (sec) 2.920000 now iterating at: 11:35:07 rms-change max change #iterations 10.76122 396.4819 at 10iterations 6.302473 122.5729 at 20iterations 3.689307 73.12634 at 30iterations 2.155625 38.60383 at 40iterations 1.260774 22.03753 at 50iterations 0.7348047 12.69542 at 60iterations 0.4293396 7.072083 at 70iterations 0.2508934 4.001707 at 80iterations 0.1459093 2.426538 at 90iterations 8.5221700E-02 1.384307 at 100iterations 4.9770374E-02 0.8082714 at 110iterations 2.8974336E-02 0.4962959 at 120iterations 1.6894357E-02 0.2805767 at 130iterations 9.8836590E-03 0.1633224 at 140iterations 5.7574245E-03 0.1018486 at 150iterations 3.3573930E-03 6.4247131E-02 at 160iterations 1.9619786E-03 3.2219887E-02 at 170iterations 1.1440453E-03 2.0101547E-02 at 180iterations finished qdiffx linear iterations at : 11:35:36 total time elapsed so far: 31.49000 # loops : 180 mean,max change (kT/e) : 1.1440453E-03 2.0101547E-02 energy calculations done at 31.49000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 31.66000 DelPhi exited at 11:35:37 31.666u 0.993s 0:33.18 98.4% 0+0k 0+0io 0pf+0w