Sun Oct 9 12:52:51 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 Sun Oct 9 2011 at 12:52:51 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 = 2412 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: 0.6927957 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): -5.953000 43.69300 ymin,ymax (A): -14.69800 36.68800 zmin,zma (A): 1.827000 44.32700 x,y,z range (A): 49.64600 51.38600 42.50000 scale (grids/A): 0.6927957 object centre (A): 18.87000 10.99500 23.07700 number of atom coordinates read : 2412 total number of charged atoms : 2270 net assigned charge : 2.500020 assigned positive charge : 367.5039 centred at (gu) : 89.38537 90.78447 90.44070 assigned negative charge : -365.0044 centred at (gu) : 89.40510 90.98361 90.52307 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7691 nv = 96 ne = 84 npr = 48948 no. pairs analyzed = 48948 no. exposed pairs = 2996 no. arc points = 20808 no. surface atoms = 1001 nbur = 1411 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 495 mr = 4245 m= 5 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.1900000 number of dielectric boundary points 3876 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1939 ## 184 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8788 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.5386628E-08 -2.0472102E-08 midg,1,midg; midg,igrid,midg 8.2476831E-08 -8.0451755E-08 1,midg,midg; igrid,midg,midg 2.6970842E-08 6.7734582E-09 gauss-seidel spectral radius is 0.9891762 estimated iterations to convergence 78 setup time was (sec) 0.3800000 now iterating at: 12:52:52 rms-change max change #iterations 0.2003152 32.72113 at 10iterations 2.3569793E-02 2.954544 at 20iterations 2.9764581E-03 0.3739929 at 30iterations 4.6704995E-04 7.6871872E-02 at 40iterations 1.0730027E-04 1.8680573E-02 at 50iterations finished qdiffx linear iterations at : 12:52:55 total time elapsed so far: 3.570000 # loops : 50 mean,max change (kT/e) : 1.0730027E-04 1.8680573E-02 energy calculations done at 3.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.700000 DelPhi exited at 12:52:56 3.700u 0.232s 0:04.47 87.9% 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 Sun Oct 9 2011 at 12:52:56 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2412 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: 2.078387 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): -5.953000 43.69300 ymin,ymax (A): -14.69800 36.68800 zmin,zma (A): 1.827000 44.32700 x,y,z range (A): 49.64600 51.38600 42.50000 scale (grids/A): 2.078387 object centre (A): 18.87000 10.99500 23.07700 number of atom coordinates read : 2412 total number of charged atoms : 2270 net assigned charge : 2.500020 assigned positive charge : 367.5039 centred at (gu) : 88.15549 92.35295 91.32154 assigned negative charge : -365.0044 centred at (gu) : 88.21493 92.95064 91.56898 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 81178 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20808 grid for indexing accessible points = 1.400000 m= 31961 mr = 56193 m= 6189 mr = 23873 m= 527 mr = 3955 m= 12 mr = 232 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 271 time to turn everything in is 0.4200000 number of dielectric boundary points 35614 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 80 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 18003 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) : 0.6927957 object centre at (A) : 18.87000 10.99500 23.07700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1083064E-02 -5.7718912E-03 midg,1,midg; midg,igrid,midg 2.7973391E-02 -6.9975264E-02 1,midg,midg; igrid,midg,midg 6.4010926E-02 -1.4147324E-04 gauss-seidel spectral radius is 0.9988259 estimated iterations to convergence 231 setup time was (sec) 0.6400000 now iterating at: 12:52:57 rms-change max change #iterations 4.853084 192.7284 at 10iterations 2.390402 88.16062 at 20iterations 1.182730 37.81578 at 30iterations 0.5820352 17.81336 at 40iterations 0.2879808 9.077920 at 50iterations 0.1424985 4.574808 at 60iterations 7.0564069E-02 2.023260 at 70iterations 3.4985218E-02 1.034196 at 80iterations 1.7387349E-02 0.5205498 at 90iterations 8.6583672E-03 0.2654877 at 100iterations 4.3460638E-03 0.1390243 at 110iterations 2.1972125E-03 6.5216064E-02 at 120iterations finished qdiffx linear iterations at : 12:53:05 total time elapsed so far: 8.060000 # loops : 120 mean,max change (kT/e) : 2.1972125E-03 6.5216064E-02 energy calculations done at 8.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.200000 DelPhi exited at 12:53:05 8.206u 0.828s 0:09.44 95.5% 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 Sun Oct 9 2011 at 12:53:05 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 = 2412 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: 3.117581 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): -5.953000 43.69300 ymin,ymax (A): -14.69800 36.68800 zmin,zma (A): 1.827000 44.32700 x,y,z range (A): 49.64600 51.38600 42.50000 scale (grids/A): 3.117581 object centre (A): 18.87000 10.99500 23.07700 number of atom coordinates read : 2412 total number of charged atoms : 2270 net assigned charge : 2.500020 assigned positive charge : 367.5039 centred at (gu) : 87.23301 93.52932 91.98219 assigned negative charge : -365.0044 centred at (gu) : 87.32226 94.42589 92.35346 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 186880 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20808 grid for indexing accessible points = 1.400000 m= 99202 mr = 135631 m= 40669 mr = 81492 m= 11623 mr = 32834 m= 2148 mr = 8828 m= 224 mr = 1475 m= 4 mr = 105 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 975 time to turn everything in is 1.320000 number of dielectric boundary points 80385 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 18160 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) : 2.078387 object centre at (A) : 18.87000 10.99500 23.07700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3960184 -0.1541304 midg,1,midg; midg,igrid,midg 0.6323678 -0.7928883 1,midg,midg; igrid,midg,midg 1.010055 -0.1704704 gauss-seidel spectral radius is 0.9993002 estimated iterations to convergence 298 setup time was (sec) 1.570000 now iterating at: 12:53:07 rms-change max change #iterations 10.94765 413.1006 at 10iterations 6.475088 130.7959 at 20iterations 3.831816 77.25032 at 30iterations 2.260576 44.46645 at 40iterations 1.329329 24.03349 at 50iterations 0.7829755 14.48059 at 60iterations 0.4599102 7.864827 at 70iterations 0.2696550 4.419875 at 80iterations 0.1578589 3.073529 at 90iterations 9.2472546E-02 1.472210 at 100iterations 5.4289129E-02 0.8963165 at 110iterations 3.1871952E-02 0.5503006 at 120iterations 1.8786373E-02 0.3242574 at 130iterations 1.1136838E-02 0.1899699 at 140iterations 6.6562733E-03 0.1188278 at 150iterations 4.0832465E-03 8.5459709E-02 at 160iterations 2.5762445E-03 5.0499916E-02 at 170iterations 1.7090547E-03 3.6771774E-02 at 180iterations finished qdiffx linear iterations at : 12:53:20 total time elapsed so far: 14.25000 # loops : 180 mean,max change (kT/e) : 1.7090547E-03 3.6771774E-02 energy calculations done at 14.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.38000 DelPhi exited at 12:53:21 14.383u 0.260s 0:15.19 96.3% 0+0k 0+0io 0pf+0w