Sat Oct 15 10:32:49 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+sph2.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 = amb2.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 10:32:49 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4438 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: 0.5862108 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): -24.47600 35.18400 ymin,ymax (A): 34.77700 95.50600 zmin,zma (A): 31.16100 89.71000 x,y,z range (A): 59.66000 60.72900 58.54900 scale (grids/A): 0.5862108 object centre (A): 5.353999 65.14150 60.43550 number of atom coordinates read : 4438 total number of charged atoms : 4279 net assigned charge : -0.9999546 assigned positive charge : 666.9171 centred at (gu) : 90.36419 89.26630 88.71413 assigned negative charge : -667.9202 centred at (gu) : 90.23038 89.41872 88.88819 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 9760 nv = 96 ne = 84 npr = 93589 no. pairs analyzed = 93589 no. exposed pairs = 4931 no. arc points = 33852 no. surface atoms = 1674 nbur = 2764 mkacc time = 0.2400000 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 = 1.456000 m= 445 mr = 5727 m= 2 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 105 time to turn everything in is 0.4900000 number of dielectric boundary points 4423 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3562 ## 400 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 12809 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.8008640E-09 -5.6438227E-09 midg,1,midg; midg,igrid,midg 6.7077632E-09 -5.6528093E-09 1,midg,midg; igrid,midg,midg -5.4487694E-09 5.3485838E-09 gauss-seidel spectral radius is 0.9850826 estimated iterations to convergence 67 setup time was (sec) 0.8200000 now iterating at: 10:32:51 rms-change max change #iterations 0.1304879 16.68639 at 10iterations 1.1110888E-02 1.316452 at 20iterations 1.2515297E-03 0.1873741 at 30iterations 2.7460381E-04 3.5709381E-02 at 40iterations 8.6235639E-05 9.3002319E-03 at 50iterations finished qdiffx linear iterations at : 10:32:55 total time elapsed so far: 5.310000 # loops : 50 mean,max change (kT/e) : 8.6235639E-05 9.3002319E-03 energy calculations done at 5.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.480000 DelPhi exited at 10:32:56 5.484u 0.477s 0:06.29 94.5% 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 10:32:56 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4438 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: 1.758633 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): -24.47600 35.18400 ymin,ymax (A): 34.77700 95.50600 zmin,zma (A): 31.16100 89.71000 x,y,z range (A): 59.66000 60.72900 58.54900 scale (grids/A): 1.758633 object centre (A): 5.353999 65.14150 60.43550 number of atom coordinates read : 4438 total number of charged atoms : 4279 net assigned charge : -0.9999546 assigned positive charge : 666.9171 centred at (gu) : 91.09132 87.79722 86.14120 assigned negative charge : -667.9202 centred at (gu) : 90.69062 88.25562 86.66400 start vw surface at 0.1600000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 108932 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33852 grid for indexing accessible points = 1.400000 m= 37933 mr = 79553 m= 5190 mr = 28329 m= 208 mr = 3250 m= 2 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.4900000 no. cavity mid-points inaccessible to solvent = 5383 time to turn everything in is 0.8900000 number of dielectric boundary points 41068 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 353 ## 1 charges are in solution ## iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 33329 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) : 0.5862108 object centre at (A) : 5.353999 65.14150 60.43550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.5689890E-02 -3.6391683E-02 midg,1,midg; midg,igrid,midg 3.2339752E-02 -2.1386458E-02 1,midg,midg; igrid,midg,midg -6.7733424E-03 3.4679640E-02 gauss-seidel spectral radius is 0.9985651 estimated iterations to convergence 209 setup time was (sec) 1.250000 now iterating at: 10:32:58 rms-change max change #iterations 4.926390 166.4819 at 10iterations 2.253841 62.93904 at 20iterations 1.037131 28.29383 at 30iterations 0.4780478 13.45752 at 40iterations 0.2207198 5.839613 at 50iterations 0.1013858 2.697002 at 60iterations 4.6770681E-02 1.283051 at 70iterations 2.1637935E-02 0.6159821 at 80iterations 9.9870022E-03 0.2787895 at 90iterations 4.6502715E-03 0.1424475 at 100iterations 2.1854786E-03 6.2469482E-02 at 110iterations 1.0394141E-03 2.9445648E-02 at 120iterations finished qdiffx linear iterations at : 10:33:10 total time elapsed so far: 13.29000 # loops : 120 mean,max change (kT/e) : 1.0394141E-03 2.9445648E-02 energy calculations done at 13.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.47000 DelPhi exited at 10:33:10 13.471u 0.529s 0:14.37 97.3% 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 10:33:10 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: 249 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4438 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: 2.637949 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): -24.47600 35.18400 ymin,ymax (A): 34.77700 95.50600 zmin,zma (A): 31.16100 89.71000 x,y,z range (A): 59.66000 60.72900 58.54900 scale (grids/A): 2.637949 object centre (A): 5.353999 65.14150 60.43550 number of atom coordinates read : 4438 total number of charged atoms : 4279 net assigned charge : -0.9999546 assigned positive charge : 666.9171 centred at (gu) : 91.63673 86.69572 84.21136 assigned negative charge : -667.9202 centred at (gu) : 91.03576 87.38339 84.99590 start vw surface at 0.1600000 fill in re-entrant regions at 0.7100000 boundary points on vw surface= 253210 reading accessible surface arcs data from file ARCDAT no. of arc points read = 33852 grid for indexing accessible points = 1.400000 m= 126895 mr = 192531 m= 42004 mr = 105447 m= 8946 mr = 33888 m= 1033 mr = 6886 m= 35 mr = 667 m= 0 mr = 7 time to grow re-entrant surface = 1.440000 no. cavity mid-points inaccessible to solvent = 17989 time to turn everything in is 2.310000 number of dielectric boundary points 92697 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 2.490000 number of grid points assigned charge 34228 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) : 1.758633 object centre at (A) : 5.353999 65.14150 60.43550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9798912 -0.4452840 midg,1,midg; midg,igrid,midg 0.3743445 -0.3515886 1,midg,midg; igrid,midg,midg -1.1306443E-02 0.2705880 gauss-seidel spectral radius is 0.9992672 estimated iterations to convergence 292 setup time was (sec) 2.740000 now iterating at: 10:33:13 rms-change max change #iterations 11.98898 326.9610 at 10iterations 7.076214 136.7404 at 20iterations 4.135868 81.24525 at 30iterations 2.416557 54.30947 at 40iterations 1.407111 23.52904 at 50iterations 0.8167784 13.21772 at 60iterations 0.4726985 8.070408 at 70iterations 0.2742482 4.085449 at 80iterations 0.1587691 2.665945 at 90iterations 9.1934822E-02 1.570843 at 100iterations 5.3054065E-02 0.8498392 at 110iterations 3.0694555E-02 0.4729366 at 120iterations 1.7767213E-02 0.2826920 at 130iterations 1.0277811E-02 0.1588974 at 140iterations 5.9577283E-03 9.0228081E-02 at 150iterations 3.4665044E-03 5.4365158E-02 at 160iterations 2.0320769E-03 3.1508446E-02 at 170iterations 1.2032459E-03 1.8074036E-02 at 180iterations finished qdiffx linear iterations at : 10:33:34 total time elapsed so far: 23.31000 # loops : 180 mean,max change (kT/e) : 1.2032459E-03 1.8074036E-02 energy calculations done at 23.31000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 23.48000 DelPhi exited at 10:33:35 23.487u 0.560s 0:24.44 98.3% 0+0k 0+0io 0pf+0w