Sun Oct 9 01:58:36 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+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 Sun Oct 9 2011 at 01:58:37 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3232 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 0.5572601 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): -40.13400 16.39300 ymin,ymax (A): -13.58000 50.30400 zmin,zma (A): -48.23300 9.346000 x,y,z range (A): 56.52700 63.88400 57.57900 scale (grids/A): 0.5572601 object centre (A): -11.87050 18.36200 -19.44350 number of atom coordinates read : 3232 total number of charged atoms : 3090 net assigned charge : 15.72602 assigned positive charge : 477.7427 centred at (gu) : 90.09103 90.75173 91.59396 assigned negative charge : -462.0184 centred at (gu) : 90.24308 90.72449 91.79661 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6824 nv = 96 ne = 84 npr = 62773 no. pairs analyzed = 62773 no. exposed pairs = 4283 no. arc points = 30879 no. surface atoms = 1419 nbur = 1813 mkacc time = 0.1700000 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= 278 mr = 3414 m= 1 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 3673 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3217 ## 417 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 8784 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4565785E-09 -9.6039998E-10 midg,1,midg; midg,igrid,midg 1.0589848E-09 2.1864897E-09 1,midg,midg; igrid,midg,midg 3.0295395E-09 -6.9091136E-11 gauss-seidel spectral radius is 0.9834239 estimated iterations to convergence 64 setup time was (sec) 0.6700000 now iterating at: 01:58:37 rms-change max change #iterations 8.5394867E-02 12.74057 at 10iterations 5.7387198E-03 0.8345718 at 20iterations 4.2840873E-04 6.4081192E-02 at 30iterations 3.7447422E-05 4.8789978E-03 at 40iterations 4.5318920E-06 5.3215027E-04 at 50iterations finished qdiffx linear iterations at : 01:58:41 total time elapsed so far: 3.950000 # loops : 50 mean,max change (kT/e) : 4.5318920E-06 5.3215027E-04 energy calculations done at 3.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.130000 DelPhi exited at 01:58:41 4.133u 0.259s 0:04.73 92.6% 0+0k 0+0io 6pf+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 Sun Oct 9 2011 at 01:58:41 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3232 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 1.671780 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): -40.13400 16.39300 ymin,ymax (A): -13.58000 50.30400 zmin,zma (A): -48.23300 9.346000 x,y,z range (A): 56.52700 63.88400 57.57900 scale (grids/A): 1.671780 object centre (A): -11.87050 18.36200 -19.44350 number of atom coordinates read : 3232 total number of charged atoms : 3090 net assigned charge : 15.72602 assigned positive charge : 477.7427 centred at (gu) : 90.27222 92.25469 94.78137 assigned negative charge : -462.0184 centred at (gu) : 90.72908 92.17323 95.38953 start vw surface at 0.1700000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 75311 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30879 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 23684 mr = 50183 m= 2695 mr = 16263 m= 84 mr = 1380 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 421 time to turn everything in is 0.6700000 number of dielectric boundary points 33944 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 378 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 23806 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) : 0.5572601 object centre at (A) : -11.87050 18.36200 -19.44350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1068482E-02 1.2125592E-02 midg,1,midg; midg,igrid,midg 2.2396637E-02 4.0493660E-02 1,midg,midg; igrid,midg,midg 1.6867997E-02 -3.7805638E-03 gauss-seidel spectral radius is 0.9983152 estimated iterations to convergence 193 setup time was (sec) 0.9700000 now iterating at: 01:58:43 rms-change max change #iterations 3.611492 148.6206 at 10iterations 1.541651 60.64936 at 20iterations 0.6589180 24.98213 at 30iterations 0.2836567 10.19325 at 40iterations 0.1222680 4.095438 at 50iterations 5.2355140E-02 1.768833 at 60iterations 2.2552997E-02 0.7363701 at 70iterations 9.6941805E-03 0.3208184 at 80iterations 4.1572168E-03 0.1399879 at 90iterations 1.7888913E-03 7.2116852E-02 at 100iterations 7.7306223E-04 2.5844574E-02 at 110iterations 3.3272861E-04 1.2252808E-02 at 120iterations finished qdiffx linear iterations at : 01:58:51 total time elapsed so far: 9.290000 # loops : 120 mean,max change (kT/e) : 3.3272861E-04 1.2252808E-02 energy calculations done at 9.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.470000 DelPhi exited at 01:58:51 9.469u 0.290s 0:10.07 96.8% 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 Sun Oct 9 2011 at 01:58:51 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: 247 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3232 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 2.507670 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): -40.13400 16.39300 ymin,ymax (A): -13.58000 50.30400 zmin,zma (A): -48.23300 9.346000 x,y,z range (A): 56.52700 63.88400 57.57900 scale (grids/A): 2.507670 object centre (A): -11.87050 18.36200 -19.44350 number of atom coordinates read : 3232 total number of charged atoms : 3090 net assigned charge : 15.72602 assigned positive charge : 477.7427 centred at (gu) : 90.40806 93.38168 97.17162 assigned negative charge : -462.0184 centred at (gu) : 91.09342 93.25980 98.08412 start vw surface at 0.1800000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 174550 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30879 grid for indexing accessible points = 1.400000 m= 80771 mr = 122724 m= 24182 mr = 63460 m= 4315 mr = 18273 m= 361 mr = 2874 m= 4 mr = 179 m= 0 mr = 0 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 1328 time to turn everything in is 1.630000 number of dielectric boundary points 76673 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 1.780000 number of grid points assigned charge 24683 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) : 1.671780 object centre at (A) : -11.87050 18.36200 -19.44350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4621022 0.1503628 midg,1,midg; midg,igrid,midg 0.4316261 0.6626022 1,midg,midg; igrid,midg,midg 0.2367294 -1.6906373E-02 gauss-seidel spectral radius is 0.9991931 estimated iterations to convergence 278 setup time was (sec) 1.960000 now iterating at: 01:58:54 rms-change max change #iterations 9.354437 313.4442 at 10iterations 5.419251 138.9963 at 20iterations 3.099667 71.75201 at 30iterations 1.764390 41.21185 at 40iterations 1.001189 24.62780 at 50iterations 0.5661469 12.82493 at 60iterations 0.3198167 6.726553 at 70iterations 0.1803582 3.535107 at 80iterations 0.1013284 2.194537 at 90iterations 5.6940757E-02 1.246161 at 100iterations 3.1990677E-02 0.6316748 at 110iterations 1.7965011E-02 0.3693824 at 120iterations 1.0049492E-02 0.1931057 at 130iterations 5.6504081E-03 0.1260376 at 140iterations 3.1579547E-03 6.7405701E-02 at 150iterations 1.7687973E-03 3.3211768E-02 at 160iterations 9.9195191E-04 2.0196915E-02 at 170iterations 5.5646466E-04 1.0497093E-02 at 180iterations finished qdiffx linear iterations at : 01:59:07 total time elapsed so far: 15.72000 # loops : 180 mean,max change (kT/e) : 5.5646466E-04 1.0497093E-02 energy calculations done at 15.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.90000 DelPhi exited at 01:59:08 15.900u 0.310s 0:16.47 98.4% 0+0k 0+0io 0pf+0w