Mon Oct 10 18:32:54 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 18:32:54 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 = 2402 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: 0.6793764 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): 28.76700 74.71100 ymin,ymax (A): 98.54100 146.7990 zmin,zma (A): 31.33400 83.73500 x,y,z range (A): 45.94400 48.25800 52.40100 scale (grids/A): 0.6793764 object centre (A): 51.73900 122.6700 57.53450 number of atom coordinates read : 2402 total number of charged atoms : 2265 net assigned charge : 1.000006 assigned positive charge : 357.9059 centred at (gu) : 89.09093 87.79176 89.31904 assigned negative charge : -356.9065 centred at (gu) : 89.00536 87.90306 89.29595 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7411 nv = 96 ne = 84 npr = 49793 no. pairs analyzed = 49793 no. exposed pairs = 2880 no. arc points = 19997 no. surface atoms = 971 nbur = 1431 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 437 mr = 4244 m= 2 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 51 time to turn everything in is 0.3100000 number of dielectric boundary points 3533 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1818 ## 157 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 8514 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.5458192E-09 9.1385131E-09 midg,1,midg; midg,igrid,midg 5.6978404E-08 -1.8554642E-08 1,midg,midg; igrid,midg,midg -2.6103228E-08 2.3742368E-08 gauss-seidel spectral radius is 0.9887471 estimated iterations to convergence 77 setup time was (sec) 0.5500000 now iterating at: 18:32:55 rms-change max change #iterations 0.1828327 25.42212 at 10iterations 2.0664163E-02 2.687218 at 20iterations 2.5441174E-03 0.3806458 at 30iterations 3.9942082E-04 6.3234329E-02 at 40iterations 9.6561853E-05 1.5307426E-02 at 50iterations finished qdiffx linear iterations at : 18:32:57 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 9.6561853E-05 1.5307426E-02 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 18:32:58 3.563u 0.198s 0:04.19 89.4% 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 18:32:58 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 = 2402 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: 2.038129 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): 28.76700 74.71100 ymin,ymax (A): 98.54100 146.7990 zmin,zma (A): 31.33400 83.73500 x,y,z range (A): 45.94400 48.25800 52.40100 scale (grids/A): 2.038129 object centre (A): 51.73900 122.6700 57.53450 number of atom coordinates read : 2402 total number of charged atoms : 2265 net assigned charge : 1.000006 assigned positive charge : 357.9059 centred at (gu) : 87.27229 83.37482 87.95668 assigned negative charge : -356.9065 centred at (gu) : 87.01579 83.70895 87.88780 start vw surface at 0.1600000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 79081 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19997 grid for indexing accessible points = 1.400000 m= 31308 mr = 55958 m= 6026 mr = 23965 m= 418 mr = 4134 m= 7 mr = 209 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 1453 time to turn everything in is 0.6500000 number of dielectric boundary points 32574 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 95 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 17950 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) : 0.6793764 object centre at (A) : 51.73900 122.6700 57.53450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.6112407E-04 1.9909712E-02 midg,1,midg; midg,igrid,midg 3.1265415E-02 -9.5735267E-03 1,midg,midg; igrid,midg,midg -3.4374264E-03 1.3396938E-02 gauss-seidel spectral radius is 0.9987749 estimated iterations to convergence 226 setup time was (sec) 0.9500000 now iterating at: 18:32:59 rms-change max change #iterations 4.627714 212.2564 at 10iterations 2.248391 73.08604 at 20iterations 1.097692 33.50499 at 30iterations 0.5345467 16.51296 at 40iterations 0.2614930 7.672335 at 50iterations 0.1281100 4.210702 at 60iterations 6.2583536E-02 1.782089 at 70iterations 3.0560644E-02 0.8826866 at 80iterations 1.4952875E-02 0.4569778 at 90iterations 7.3676961E-03 0.2193856 at 100iterations 3.6441879E-03 0.1023388 at 110iterations 1.8432949E-03 5.2822828E-02 at 120iterations finished qdiffx linear iterations at : 18:33:06 total time elapsed so far: 7.940000 # loops : 120 mean,max change (kT/e) : 1.8432949E-03 5.2822828E-02 energy calculations done at 7.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.140000 DelPhi exited at 18:33:07 8.140u 0.251s 0:09.00 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 18:33:07 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 = 2402 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: 3.057194 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): 28.76700 74.71100 ymin,ymax (A): 98.54100 146.7990 zmin,zma (A): 31.33400 83.73500 x,y,z range (A): 45.94400 48.25800 52.40100 scale (grids/A): 3.057194 object centre (A): 51.73900 122.6700 57.53450 number of atom coordinates read : 2402 total number of charged atoms : 2265 net assigned charge : 1.000006 assigned positive charge : 357.9059 centred at (gu) : 85.90820 80.06202 86.93499 assigned negative charge : -356.9065 centred at (gu) : 85.52354 80.56329 86.83154 start vw surface at 0.1400000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 182530 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19997 grid for indexing accessible points = 1.400000 m= 97296 mr = 134644 m= 40199 mr = 81372 m= 11221 mr = 33468 m= 1894 mr = 8881 m= 179 mr = 1404 m= 2 mr = 100 m= 0 mr = 0 time to grow re-entrant surface = 0.9500000 no. cavity mid-points inaccessible to solvent = 4720 time to turn everything in is 1.610000 number of dielectric boundary points 73452 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 18116 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) : 2.038129 object centre at (A) : 51.73900 122.6700 57.53450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4080066 0.7823884 midg,1,midg; midg,igrid,midg 0.2271498 -9.1398060E-02 1,midg,midg; igrid,midg,midg 1.6285382E-02 4.1489653E-02 gauss-seidel spectral radius is 0.9992882 estimated iterations to convergence 296 setup time was (sec) 1.940000 now iterating at: 18:33:09 rms-change max change #iterations 10.45259 421.9694 at 10iterations 6.110329 131.3606 at 20iterations 3.569150 74.51845 at 30iterations 2.084952 38.19582 at 40iterations 1.213300 25.35978 at 50iterations 0.7063605 12.10487 at 60iterations 0.4118604 7.624090 at 70iterations 0.2394478 4.161131 at 80iterations 0.1392328 2.814653 at 90iterations 8.1001788E-02 1.470272 at 100iterations 4.7143247E-02 0.8054657 at 110iterations 2.7381158E-02 0.4492822 at 120iterations 1.5925618E-02 0.2780437 at 130iterations 9.2816446E-03 0.1657505 at 140iterations 5.4100105E-03 0.1116104 at 150iterations 3.1584727E-03 5.9196711E-02 at 160iterations 1.8664683E-03 3.1490326E-02 at 170iterations 1.1167997E-03 2.1467209E-02 at 180iterations finished qdiffx linear iterations at : 18:33:20 total time elapsed so far: 13.10000 # loops : 180 mean,max change (kT/e) : 1.1167997E-03 2.1467209E-02 energy calculations done at 13.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.31000 DelPhi exited at 18:33:21 13.310u 0.247s 0:14.26 95.0% 0+0k 0+0io 0pf+0w