Tue Oct 11 01:08:42 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 Tue Oct 11 2011 at 01:08:43 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2607 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: 0.6251207 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): -3.800000 53.14900 ymin,ymax (A): 5.408000 58.79500 zmin,zma (A): 7.740000 50.75100 x,y,z range (A): 56.94900 53.38700 43.01100 scale (grids/A): 0.6251207 object centre (A): 24.67450 32.10150 29.24550 number of atom coordinates read : 2607 total number of charged atoms : 2464 net assigned charge : 3.000010 assigned positive charge : 393.4349 centred at (gu) : 89.64076 89.08923 90.16037 assigned negative charge : -390.4352 centred at (gu) : 89.72437 89.06287 90.33824 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6841 nv = 96 ne = 84 npr = 52817 no. pairs analyzed = 52817 no. exposed pairs = 3120 no. arc points = 22049 no. surface atoms = 1056 nbur = 1551 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 340 mr = 3823 m= 1 mr = 35 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 42 time to turn everything in is 0.3100000 number of dielectric boundary points 3324 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2102 ## 208 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8183 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5793720E-08 -1.1612642E-08 midg,1,midg; midg,igrid,midg 9.5378361E-10 4.0208028E-09 1,midg,midg; igrid,midg,midg 1.0032770E-08 -3.3872471E-09 gauss-seidel spectral radius is 0.9867469 estimated iterations to convergence 71 setup time was (sec) 0.6000000 now iterating at: 01:08:44 rms-change max change #iterations 0.1364174 19.00361 at 10iterations 1.3638738E-02 1.857601 at 20iterations 2.1089099E-03 0.4228554 at 30iterations 5.7767762E-04 0.1310997 at 40iterations 1.8174345E-04 4.2179108E-02 at 50iterations finished qdiffx linear iterations at : 01:08:47 total time elapsed so far: 4.290000 # loops : 50 mean,max change (kT/e) : 1.8174345E-04 4.2179108E-02 energy calculations done at 4.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.460000 DelPhi exited at 01:08:48 4.461u 0.377s 0:05.25 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 Tue Oct 11 2011 at 01:08:48 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2607 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: 1.875362 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): -3.800000 53.14900 ymin,ymax (A): 5.408000 58.79500 zmin,zma (A): 7.740000 50.75100 x,y,z range (A): 56.94900 53.38700 43.01100 scale (grids/A): 1.875362 object centre (A): 24.67450 32.10150 29.24550 number of atom coordinates read : 2607 total number of charged atoms : 2464 net assigned charge : 3.000010 assigned positive charge : 393.4349 centred at (gu) : 88.92176 87.26717 90.48080 assigned negative charge : -390.4352 centred at (gu) : 89.17277 87.18832 91.01460 start vw surface at 0.1200000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 74176 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22049 grid for indexing accessible points = 1.400000 m= 26121 mr = 52082 m= 3842 mr = 19204 m= 205 mr = 2379 m= 2 mr = 54 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 2066 time to turn everything in is 0.5900000 number of dielectric boundary points 30627 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 152 iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 19338 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) : 0.6251207 object centre at (A) : 24.67450 32.10150 29.24550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0513389E-02 2.8145823E-03 midg,1,midg; midg,igrid,midg -4.4648424E-03 5.1137141E-04 1,midg,midg; igrid,midg,midg -3.7543969E-03 -2.1765171E-02 gauss-seidel spectral radius is 0.9985934 estimated iterations to convergence 211 setup time was (sec) 0.8800000 now iterating at: 01:08:49 rms-change max change #iterations 4.167569 174.0107 at 10iterations 1.920087 71.52717 at 20iterations 0.8865102 33.22531 at 30iterations 0.4107290 13.56569 at 40iterations 0.1903998 6.396858 at 50iterations 8.8490285E-02 2.868641 at 60iterations 4.1109636E-02 1.299980 at 70iterations 1.9214140E-02 0.5959969 at 80iterations 9.1178408E-03 0.3220062 at 90iterations 4.3979743E-03 0.1437492 at 100iterations 2.1964652E-03 9.0480804E-02 at 110iterations 1.1733723E-03 5.3680420E-02 at 120iterations finished qdiffx linear iterations at : 01:08:59 total time elapsed so far: 10.30000 # loops : 120 mean,max change (kT/e) : 1.1733723E-03 5.3680420E-02 energy calculations done at 10.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.47000 DelPhi exited at 01:08:59 10.473u 0.437s 0:11.50 94.7% 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 Tue Oct 11 2011 at 01:08:59 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2607 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: 2.813043 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): -3.800000 53.14900 ymin,ymax (A): 5.408000 58.79500 zmin,zma (A): 7.740000 50.75100 x,y,z range (A): 56.94900 53.38700 43.01100 scale (grids/A): 2.813043 object centre (A): 24.67450 32.10150 29.24550 number of atom coordinates read : 2607 total number of charged atoms : 2464 net assigned charge : 3.000010 assigned positive charge : 393.4349 centred at (gu) : 88.38264 85.90052 90.72117 assigned negative charge : -390.4352 centred at (gu) : 88.75906 85.78240 91.52171 start vw surface at 0.1200000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 171910 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22049 grid for indexing accessible points = 1.400000 m= 85992 mr = 126059 m= 29629 mr = 70699 m= 6665 mr = 23738 m= 869 mr = 4961 m= 44 mr = 532 m= 2 mr = 21 m= 0 mr = 2 time to grow re-entrant surface = 0.9300000 no. cavity mid-points inaccessible to solvent = 6721 time to turn everything in is 1.540000 number of dielectric boundary points 69099 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 19709 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) : 1.875362 object centre at (A) : 24.67450 32.10150 29.24550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3106777 8.4920049E-02 midg,1,midg; midg,igrid,midg 0.2297305 -4.7095895E-02 1,midg,midg; igrid,midg,midg -3.7139643E-02 -0.1930108 gauss-seidel spectral radius is 0.9992419 estimated iterations to convergence 287 setup time was (sec) 1.920000 now iterating at: 01:09:02 rms-change max change #iterations 9.710780 299.8789 at 10iterations 5.597029 116.4959 at 20iterations 3.204941 71.38258 at 30iterations 1.835513 41.77655 at 40iterations 1.051155 20.05733 at 50iterations 0.6007192 11.43036 at 60iterations 0.3424467 7.232041 at 70iterations 0.1952014 4.175394 at 80iterations 0.1114252 2.225571 at 90iterations 6.3715801E-02 1.115753 at 100iterations 3.6372416E-02 0.6676416 at 110iterations 2.0839266E-02 0.3856535 at 120iterations 1.1931702E-02 0.2518616 at 130iterations 6.9119013E-03 0.1404858 at 140iterations 4.0452974E-03 7.7659607E-02 at 150iterations 2.4043203E-03 5.4569244E-02 at 160iterations 1.4840927E-03 3.6113739E-02 at 170iterations 9.6338475E-04 2.2281647E-02 at 180iterations finished qdiffx linear iterations at : 01:09:18 total time elapsed so far: 18.24000 # loops : 180 mean,max change (kT/e) : 9.6338475E-04 2.2281647E-02 energy calculations done at 18.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.40000 DelPhi exited at 01:09:19 18.403u 0.467s 0:19.16 98.4% 0+0k 0+0io 0pf+0w