Mon Oct 10 00:08:44 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+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 Mon Oct 10 2011 at 00:08:44 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3121 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6320574 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): -34.85600 19.46500 ymin,ymax (A): -13.49100 37.69400 zmin,zma (A): -14.55100 41.77300 x,y,z range (A): 54.32100 51.18500 56.32400 scale (grids/A): 0.6320574 object centre (A): -7.695501 12.10150 13.61100 number of atom coordinates read : 3121 total number of charged atoms : 2978 net assigned charge : 1.500007 assigned positive charge : 470.6719 centred at (gu) : 91.01610 90.46087 91.36753 assigned negative charge : -469.1732 centred at (gu) : 90.98714 90.37664 91.30755 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8406 nv = 96 ne = 84 npr = 61652 no. pairs analyzed = 61652 no. exposed pairs = 4033 no. arc points = 29055 no. surface atoms = 1339 nbur = 1782 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 426 mr = 4482 m= 2 mr = 38 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 28 time to turn everything in is 0.3300000 number of dielectric boundary points 4314 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2850 ## 278 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 10179 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.8911963E-09 1.1180080E-08 midg,1,midg; midg,igrid,midg -7.2741329E-09 1.2137590E-08 1,midg,midg; igrid,midg,midg -1.3748904E-09 5.9946892E-09 gauss-seidel spectral radius is 0.9870862 estimated iterations to convergence 72 setup time was (sec) 0.5400000 now iterating at: 00:08:45 rms-change max change #iterations 0.1488686 19.80316 at 10iterations 1.4522917E-02 1.938612 at 20iterations 1.3972042E-03 0.1996899 at 30iterations 1.3590949E-04 1.8917084E-02 at 40iterations 1.3998211E-05 1.7700195E-03 at 50iterations finished qdiffx linear iterations at : 00:08:48 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 1.3998211E-05 1.7700195E-03 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 00:08:48 3.112u 0.152s 0:03.58 91.0% 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 00:08:48 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3121 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.896172 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): -34.85600 19.46500 ymin,ymax (A): -13.49100 37.69400 zmin,zma (A): -14.55100 41.77300 x,y,z range (A): 54.32100 51.18500 56.32400 scale (grids/A): 1.896172 object centre (A): -7.695501 12.10150 13.61100 number of atom coordinates read : 3121 total number of charged atoms : 2978 net assigned charge : 1.500007 assigned positive charge : 470.6719 centred at (gu) : 93.04744 91.38180 94.10198 assigned negative charge : -469.1732 centred at (gu) : 92.96121 91.12971 93.92246 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 91088 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29055 grid for indexing accessible points = 1.400000 m= 30805 mr = 62130 m= 4442 mr = 22073 m= 235 mr = 2574 m= 2 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 3108 time to turn everything in is 0.6100000 number of dielectric boundary points 39716 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 203 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 23415 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) : 0.6320574 object centre at (A) : -7.695501 12.10150 13.61100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9356142E-03 -6.2717707E-04 midg,1,midg; midg,igrid,midg -8.3065941E-04 1.6216740E-02 1,midg,midg; igrid,midg,midg -1.7233524E-02 4.2898236E-03 gauss-seidel spectral radius is 0.9986857 estimated iterations to convergence 219 setup time was (sec) 0.8700000 now iterating at: 00:08:49 rms-change max change #iterations 4.634337 186.5324 at 10iterations 2.195897 64.87196 at 20iterations 1.040644 32.96199 at 30iterations 0.4925910 15.11312 at 40iterations 0.2343456 7.359276 at 50iterations 0.1109988 3.310262 at 60iterations 5.2688446E-02 1.646471 at 70iterations 2.5047503E-02 0.7520142 at 80iterations 1.1884527E-02 0.3357391 at 90iterations 5.6483559E-03 0.1671562 at 100iterations 2.6794656E-03 8.7454319E-02 at 110iterations 1.2733142E-03 3.6630630E-02 at 120iterations finished qdiffx linear iterations at : 00:08:55 total time elapsed so far: 6.900000 # loops : 120 mean,max change (kT/e) : 1.2733142E-03 3.6630630E-02 energy calculations done at 6.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.080000 DelPhi exited at 00:08:56 7.084u 0.151s 0:07.56 95.6% 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 00:08:56 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3121 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: 2.844258 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): -34.85600 19.46500 ymin,ymax (A): -13.49100 37.69400 zmin,zma (A): -14.55100 41.77300 x,y,z range (A): 54.32100 51.18500 56.32400 scale (grids/A): 2.844258 object centre (A): -7.695501 12.10150 13.61100 number of atom coordinates read : 3121 total number of charged atoms : 2978 net assigned charge : 1.500007 assigned positive charge : 470.6719 centred at (gu) : 94.57114 92.07246 96.15264 assigned negative charge : -469.1732 centred at (gu) : 94.44168 91.69459 95.88354 start vw surface at 0.1700000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 211046 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29055 grid for indexing accessible points = 1.400000 m= 101941 mr = 151061 m= 34302 mr = 82334 m= 7694 mr = 26817 m= 1028 mr = 5540 m= 46 mr = 648 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.8800000 no. cavity mid-points inaccessible to solvent = 10349 time to turn everything in is 1.510000 number of dielectric boundary points 89640 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 23822 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) : 1.896172 object centre at (A) : -7.695501 12.10150 13.61100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1238952 -0.1059907 midg,1,midg; midg,igrid,midg 9.3902618E-02 -9.1504075E-02 1,midg,midg; igrid,midg,midg -0.3050061 -4.0410243E-02 gauss-seidel spectral radius is 0.9992975 estimated iterations to convergence 298 setup time was (sec) 1.800000 now iterating at: 00:08:58 rms-change max change #iterations 11.10858 318.0436 at 10iterations 6.697692 140.7360 at 20iterations 3.989912 85.63042 at 30iterations 2.371978 48.12293 at 40iterations 1.399551 27.82136 at 50iterations 0.8248190 14.88548 at 60iterations 0.4853102 8.837540 at 70iterations 0.2841282 5.093116 at 80iterations 0.1669185 2.849482 at 90iterations 9.7572684E-02 1.618631 at 100iterations 5.7066839E-02 1.080071 at 110iterations 3.3320494E-02 0.5462197 at 120iterations 1.9485861E-02 0.3358650 at 130iterations 1.1386183E-02 0.1768036 at 140iterations 6.6497112E-03 0.1174867 at 150iterations 3.8726148E-03 6.1517715E-02 at 160iterations 2.2659923E-03 3.5243034E-02 at 170iterations 1.3211897E-03 2.2842856E-02 at 180iterations finished qdiffx linear iterations at : 00:09:08 total time elapsed so far: 11.80000 # loops : 180 mean,max change (kT/e) : 1.3211897E-03 2.2842856E-02 energy calculations done at 11.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.97000 DelPhi exited at 00:09:08 11.971u 0.171s 0:12.55 96.7% 0+0k 0+0io 0pf+0w