Mon Oct 10 17:00:05 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 17:00:05 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 = 2831 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6017274 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): -27.05700 32.10600 ymin,ymax (A): -11.82500 38.80200 zmin,zma (A): 5.665000 60.18400 x,y,z range (A): 59.16300 50.62700 54.51900 scale (grids/A): 0.6017274 object centre (A): 2.524500 13.48850 32.92450 number of atom coordinates read : 2831 total number of charged atoms : 2690 net assigned charge : -3.499969 assigned positive charge : 426.0852 centred at (gu) : 90.99641 91.01981 91.45119 assigned negative charge : -429.5863 centred at (gu) : 91.09124 90.90202 91.52664 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6775 nv = 96 ne = 84 npr = 56968 no. pairs analyzed = 56968 no. exposed pairs = 3806 no. arc points = 26235 no. surface atoms = 1269 nbur = 1562 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 342 mr = 3468 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.2100000 number of dielectric boundary points 3638 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2748 ## 304 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8499 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1573293E-09 -6.6352039E-09 midg,1,midg; midg,igrid,midg -5.2354241E-09 4.3252433E-09 1,midg,midg; igrid,midg,midg 1.9311603E-09 -7.0316357E-09 gauss-seidel spectral radius is 0.9857280 estimated iterations to convergence 69 setup time was (sec) 0.3900000 now iterating at: 17:00:05 rms-change max change #iterations 0.1113613 19.36314 at 10iterations 9.5456121E-03 1.353640 at 20iterations 8.1325619E-04 0.1241150 at 30iterations 6.9190595E-05 9.1829300E-03 at 40iterations 6.1292772E-06 8.7165833E-04 at 50iterations finished qdiffx linear iterations at : 17:00:08 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 6.1292772E-06 8.7165833E-04 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.400000 DelPhi exited at 17:00:08 3.407u 0.178s 0:03.88 92.0% 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 17:00:08 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 = 2831 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.805182 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): -27.05700 32.10600 ymin,ymax (A): -11.82500 38.80200 zmin,zma (A): 5.665000 60.18400 x,y,z range (A): 59.16300 50.62700 54.51900 scale (grids/A): 1.805182 object centre (A): 2.524500 13.48850 32.92450 number of atom coordinates read : 2831 total number of charged atoms : 2690 net assigned charge : -3.499969 assigned positive charge : 426.0852 centred at (gu) : 92.98856 93.05864 94.35288 assigned negative charge : -429.5863 centred at (gu) : 93.27367 92.70576 94.57969 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 73044 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26235 grid for indexing accessible points = 1.400000 m= 23752 mr = 48713 m= 3061 mr = 16284 m= 135 mr = 1484 m= 0 mr = 29 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 322 time to turn everything in is 0.3600000 number of dielectric boundary points 33482 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 217 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 21023 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) : 0.6017274 object centre at (A) : 2.524500 13.48850 32.92450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1252400E-02 -1.6975763E-03 midg,1,midg; midg,igrid,midg -1.9470349E-02 2.7485192E-04 1,midg,midg; igrid,midg,midg 1.6912911E-02 -4.9547397E-02 gauss-seidel spectral radius is 0.9985077 estimated iterations to convergence 205 setup time was (sec) 0.5600000 now iterating at: 17:00:09 rms-change max change #iterations 3.985387 205.6121 at 10iterations 1.789720 65.91125 at 20iterations 0.8077013 27.45333 at 30iterations 0.3635218 13.40363 at 40iterations 0.1648021 5.308495 at 50iterations 7.4305631E-02 2.557776 at 60iterations 3.3468582E-02 1.143472 at 70iterations 1.5171453E-02 0.5190716 at 80iterations 6.8318285E-03 0.2224150 at 90iterations 3.0839487E-03 9.5961094E-02 at 100iterations 1.4009115E-03 4.7920227E-02 at 110iterations 6.3338823E-04 1.9378662E-02 at 120iterations finished qdiffx linear iterations at : 17:00:16 total time elapsed so far: 7.520000 # loops : 120 mean,max change (kT/e) : 6.3338823E-04 1.9378662E-02 energy calculations done at 7.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.640000 DelPhi exited at 17:00:17 7.646u 0.198s 0:08.40 93.2% 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 17:00:17 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 = 2831 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: 2.707773 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): -27.05700 32.10600 ymin,ymax (A): -11.82500 38.80200 zmin,zma (A): 5.665000 60.18400 x,y,z range (A): 59.16300 50.62700 54.51900 scale (grids/A): 2.707773 object centre (A): 2.524500 13.48850 32.92450 number of atom coordinates read : 2831 total number of charged atoms : 2690 net assigned charge : -3.499969 assigned positive charge : 426.0852 centred at (gu) : 94.48263 94.58781 96.52910 assigned negative charge : -429.5863 centred at (gu) : 94.91041 94.05851 96.86954 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 169116 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26235 grid for indexing accessible points = 1.400000 m= 79677 mr = 119084 m= 25361 mr = 62572 m= 4941 mr = 19060 m= 523 mr = 3174 m= 20 mr = 259 m= 0 mr = 1 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 1113 time to turn everything in is 0.9100000 number of dielectric boundary points 75488 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.000000 number of grid points assigned charge 21516 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) : 1.805182 object centre at (A) : 2.524500 13.48850 32.92450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4364356E-02 0.1093498 midg,1,midg; midg,igrid,midg -0.1952554 -2.6933247E-02 1,midg,midg; igrid,midg,midg 0.2126564 -0.6351320 gauss-seidel spectral radius is 0.9992379 estimated iterations to convergence 286 setup time was (sec) 1.150000 now iterating at: 17:00:18 rms-change max change #iterations 9.894312 288.6787 at 10iterations 5.818038 170.0188 at 20iterations 3.384550 92.35598 at 30iterations 1.954139 49.42048 at 40iterations 1.127478 23.33648 at 50iterations 0.6487127 12.73812 at 60iterations 0.3720384 7.971281 at 70iterations 0.2129515 3.739483 at 80iterations 0.1216334 2.312702 at 90iterations 6.9563508E-02 1.276527 at 100iterations 3.9767172E-02 0.7629060 at 110iterations 2.2633761E-02 0.3952904 at 120iterations 1.2933632E-02 0.2310505 at 130iterations 7.3687136E-03 0.1578627 at 140iterations 4.1920887E-03 7.4670792E-02 at 150iterations 2.3912564E-03 4.7882080E-02 at 160iterations 1.3626590E-03 2.4999619E-02 at 170iterations 7.7661430E-04 1.4382362E-02 at 180iterations finished qdiffx linear iterations at : 17:00:30 total time elapsed so far: 12.54000 # loops : 180 mean,max change (kT/e) : 7.7661430E-04 1.4382362E-02 energy calculations done at 12.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.67000 DelPhi exited at 17:00:31 12.676u 0.203s 0:13.47 95.5% 0+0k 0+0io 0pf+0w