Sat Oct 15 10:46:39 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 Sat Oct 15 2011 at 10:46:39 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 = 4298 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5835778 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): -25.09700 35.90600 ymin,ymax (A): 37.81500 97.67800 zmin,zma (A): 29.24800 88.22200 x,y,z range (A): 61.00300 59.86300 58.97400 scale (grids/A): 0.5835778 object centre (A): 5.404501 67.74651 58.73500 number of atom coordinates read : 4298 total number of charged atoms : 4163 net assigned charge : -5.499941 assigned positive charge : 645.3224 centred at (gu) : 90.65737 88.46927 88.90290 assigned negative charge : -650.8254 centred at (gu) : 90.50676 88.58562 89.03075 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 9445 nv = 96 ne = 84 npr = 90229 no. pairs analyzed = 90229 no. exposed pairs = 4802 no. arc points = 32699 no. surface atoms = 1630 nbur = 2668 mkacc time = 0.1900000 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 = 1.484000 m= 438 mr = 5603 m= 1 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 45 time to turn everything in is 0.4200000 number of dielectric boundary points 4227 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3413 ## 382 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 12355 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.9695500E-09 -4.8052722E-09 midg,1,midg; midg,igrid,midg 3.8344496E-09 -4.0489168E-09 1,midg,midg; igrid,midg,midg -6.0499352E-09 4.4954427E-09 gauss-seidel spectral radius is 0.9849365 estimated iterations to convergence 67 setup time was (sec) 0.6600000 now iterating at: 10:46:40 rms-change max change #iterations 0.1249454 17.17817 at 10iterations 1.0417678E-02 1.439583 at 20iterations 1.1266011E-03 0.1429176 at 30iterations 2.4867425E-04 3.0406475E-02 at 40iterations 8.1578233E-05 1.0658264E-02 at 50iterations finished qdiffx linear iterations at : 10:46:42 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 8.1578233E-05 1.0658264E-02 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 10:46:43 3.483u 0.181s 0:04.18 87.5% 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 Sat Oct 15 2011 at 10:46:43 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 = 4298 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.750733 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): -25.09700 35.90600 ymin,ymax (A): 37.81500 97.67800 zmin,zma (A): 29.24800 88.22200 x,y,z range (A): 61.00300 59.86300 58.97400 scale (grids/A): 1.750733 object centre (A): 5.404501 67.74651 58.73500 number of atom coordinates read : 4298 total number of charged atoms : 4163 net assigned charge : -5.499941 assigned positive charge : 645.3224 centred at (gu) : 91.97115 85.40673 86.70755 assigned negative charge : -650.8254 centred at (gu) : 91.51991 85.75643 87.09157 start vw surface at 0.1800000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 105411 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32699 grid for indexing accessible points = 1.400000 m= 36494 mr = 77349 m= 4800 mr = 27132 m= 165 mr = 2984 m= 3 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 4168 time to turn everything in is 0.7000000 number of dielectric boundary points 39367 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 306 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 32423 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) : 0.5835778 object centre at (A) : 5.404501 67.74651 58.73500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2866549E-02 -3.1724289E-02 midg,1,midg; midg,igrid,midg 2.8702924E-02 -7.2550443E-03 1,midg,midg; igrid,midg,midg -2.1212069E-02 3.7003793E-02 gauss-seidel spectral radius is 0.9985383 estimated iterations to convergence 207 setup time was (sec) 1.010000 now iterating at: 10:46:44 rms-change max change #iterations 4.774289 163.3129 at 10iterations 2.177843 58.86748 at 20iterations 0.9937400 29.20783 at 30iterations 0.4549704 13.19722 at 40iterations 0.2083769 5.717072 at 50iterations 9.4986543E-02 2.862934 at 60iterations 4.3613721E-02 1.230934 at 70iterations 1.9968536E-02 0.5352688 at 80iterations 9.1415569E-03 0.2671795 at 90iterations 4.2241123E-03 0.1159024 at 100iterations 1.9601220E-03 5.2141666E-02 at 110iterations 9.2416879E-04 2.7570724E-02 at 120iterations finished qdiffx linear iterations at : 10:46:51 total time elapsed so far: 7.780000 # loops : 120 mean,max change (kT/e) : 9.2416879E-04 2.7570724E-02 energy calculations done at 7.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.960000 DelPhi exited at 10:46:52 7.964u 0.212s 0:08.89 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 Sat Oct 15 2011 at 10:46:52 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 = 4298 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.626100 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): -25.09700 35.90600 ymin,ymax (A): 37.81500 97.67800 zmin,zma (A): 29.24800 88.22200 x,y,z range (A): 61.00300 59.86300 58.97400 scale (grids/A): 2.626100 object centre (A): 5.404501 67.74651 58.73500 number of atom coordinates read : 4298 total number of charged atoms : 4163 net assigned charge : -5.499941 assigned positive charge : 645.3224 centred at (gu) : 92.95628 83.10964 85.06095 assigned negative charge : -650.8254 centred at (gu) : 92.27984 83.63461 85.63718 start vw surface at 0.1700000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 245007 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32699 grid for indexing accessible points = 1.400000 m= 122934 mr = 187397 m= 39742 mr = 102143 m= 8266 mr = 31845 m= 850 mr = 6259 m= 26 mr = 508 m= 0 mr = 6 time to grow re-entrant surface = 1.070000 no. cavity mid-points inaccessible to solvent = 13834 time to turn everything in is 1.790000 number of dielectric boundary points 88667 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.960000 number of grid points assigned charge 33289 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) : 1.750733 object centre at (A) : 5.404501 67.74651 58.73500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1534542 -0.3805158 midg,1,midg; midg,igrid,midg 0.4698654 -2.3701387E-02 1,midg,midg; igrid,midg,midg -0.1433135 0.5080836 gauss-seidel spectral radius is 0.9992581 estimated iterations to convergence 290 setup time was (sec) 2.140000 now iterating at: 10:46:54 rms-change max change #iterations 11.59987 270.1323 at 10iterations 6.779789 129.6613 at 20iterations 3.927303 68.22469 at 30iterations 2.275705 40.63707 at 40iterations 1.318349 22.17591 at 50iterations 0.7592595 12.53154 at 60iterations 0.4377517 6.930677 at 70iterations 0.2521816 4.085125 at 80iterations 0.1453741 2.293360 at 90iterations 8.3509691E-02 1.570820 at 100iterations 4.8091557E-02 0.7092769 at 110iterations 2.7721033E-02 0.4573574 at 120iterations 1.5947424E-02 0.2478657 at 130iterations 9.1990260E-03 0.1419601 at 140iterations 5.3195003E-03 8.3808899E-02 at 150iterations 3.0790512E-03 4.9901962E-02 at 160iterations 1.8046394E-03 3.2585144E-02 at 170iterations 1.0703610E-03 1.7177582E-02 at 180iterations finished qdiffx linear iterations at : 10:47:05 total time elapsed so far: 13.15000 # loops : 180 mean,max change (kT/e) : 1.0703610E-03 1.7177582E-02 energy calculations done at 13.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.33000 DelPhi exited at 10:47:06 13.331u 0.212s 0:13.89 97.4% 0+0k 0+0io 0pf+0w