Sat Oct 8 18:08:30 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 8 2011 at 18:08:30 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 = 4414 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: 0.5221549 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): -29.69900 38.48000 ymin,ymax (A): -17.56300 41.31600 zmin,zma (A): -5.834000 60.24200 x,y,z range (A): 68.17900 58.87900 66.07600 scale (grids/A): 0.5221549 object centre (A): 4.390501 11.87650 27.20400 number of atom coordinates read : 4414 total number of charged atoms : 4262 net assigned charge : -6.999976 assigned positive charge : 673.0334 centred at (gu) : 91.01694 91.94957 90.23016 assigned negative charge : -680.0380 centred at (gu) : 90.99888 91.99965 90.20804 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7853 nv = 96 ne = 84 npr = 86005 no. pairs analyzed = 86005 no. exposed pairs = 5924 no. arc points = 41903 no. surface atoms = 1981 nbur = 2433 mkacc time = 0.1500000 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 = 1.652000 m= 300 mr = 3842 m= 0 mr = 11 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 4300 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4253 ## 646 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 10523 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3440780E-10 -7.6563700E-11 midg,1,midg; midg,igrid,midg 2.0536779E-11 -5.9914268E-10 1,midg,midg; igrid,midg,midg -1.7969874E-10 -1.1328121E-10 gauss-seidel spectral radius is 0.9812264 estimated iterations to convergence 60 setup time was (sec) 0.4900000 now iterating at: 18:08:30 rms-change max change #iterations 7.2489113E-02 11.13916 at 10iterations 4.4954452E-03 0.6017551 at 20iterations 4.4786013E-04 9.1522217E-02 at 30iterations 1.0808563E-04 2.0550728E-02 at 40iterations 3.1477182E-05 6.0853958E-03 at 50iterations finished qdiffx linear iterations at : 18:08:34 total time elapsed so far: 3.520000 # loops : 50 mean,max change (kT/e) : 3.1477182E-05 6.0853958E-03 energy calculations done at 3.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.650000 DelPhi exited at 18:08:34 3.650u 0.195s 0:04.19 91.6% 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 8 2011 at 18:08:34 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 = 4414 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: 1.566465 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): -29.69900 38.48000 ymin,ymax (A): -17.56300 41.31600 zmin,zma (A): -5.834000 60.24200 x,y,z range (A): 68.17900 58.87900 66.07600 scale (grids/A): 1.566465 object centre (A): 4.390501 11.87650 27.20400 number of atom coordinates read : 4414 total number of charged atoms : 4262 net assigned charge : -6.999976 assigned positive charge : 673.0334 centred at (gu) : 93.04956 95.84705 90.68887 assigned negative charge : -680.0380 centred at (gu) : 92.99630 95.99881 90.62411 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 87447 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41903 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 25619 mr = 57518 m= 2318 mr = 16686 m= 59 mr = 971 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 198 time to turn everything in is 0.4400000 number of dielectric boundary points 40268 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 582 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 32309 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) : 0.5221549 object centre at (A) : 4.390501 11.87650 27.20400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.9110572E-03 -1.9491571E-03 midg,1,midg; midg,igrid,midg -5.5978424E-03 -1.4460526E-02 1,midg,midg; igrid,midg,midg -4.8346738E-03 3.6595450E-03 gauss-seidel spectral radius is 0.9981717 estimated iterations to convergence 186 setup time was (sec) 0.6800000 now iterating at: 18:08:35 rms-change max change #iterations 3.828303 174.0205 at 10iterations 1.582999 54.91138 at 20iterations 0.6554778 23.86737 at 30iterations 0.2715976 10.39067 at 40iterations 0.1126798 3.477394 at 50iterations 4.6819363E-02 1.738270 at 60iterations 1.9436054E-02 0.6261463 at 70iterations 8.1576547E-03 0.2479553 at 80iterations 3.4296052E-03 0.1128635 at 90iterations 1.4629788E-03 4.9936295E-02 at 100iterations 6.4916920E-04 2.4272919E-02 at 110iterations 3.0755863E-04 1.1407495E-02 at 120iterations finished qdiffx linear iterations at : 18:08:42 total time elapsed so far: 8.140000 # loops : 120 mean,max change (kT/e) : 3.0755863E-04 1.1407495E-02 energy calculations done at 8.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.270000 DelPhi exited at 18:08:43 8.271u 0.217s 0:08.76 96.8% 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 8 2011 at 18:08:43 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4414 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: 2.349697 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): -29.69900 38.48000 ymin,ymax (A): -17.56300 41.31600 zmin,zma (A): -5.834000 60.24200 x,y,z range (A): 68.17900 58.87900 66.07600 scale (grids/A): 2.349697 object centre (A): 4.390501 11.87650 27.20400 number of atom coordinates read : 4414 total number of charged atoms : 4262 net assigned charge : -6.999976 assigned positive charge : 673.0334 centred at (gu) : 94.57410 98.77023 91.03333 assigned negative charge : -680.0380 centred at (gu) : 94.49442 98.99818 90.93593 start vw surface at 0.1200000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 203697 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41903 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 90772 mr = 141993 m= 23393 mr = 69874 m= 3198 mr = 16606 m= 191 mr = 1819 m= 3 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 659 time to turn everything in is 1.060000 number of dielectric boundary points 90902 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 60 iepsmp to db, and charging done at 1.170000 number of grid points assigned charge 34029 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) : 1.566465 object centre at (A) : 4.390501 11.87650 27.20400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1527071 -8.0727199E-03 midg,1,midg; midg,igrid,midg -5.9057947E-02 -0.2065260 1,midg,midg; igrid,midg,midg -7.6894790E-02 2.4639057E-02 gauss-seidel spectral radius is 0.9991640 estimated iterations to convergence 273 setup time was (sec) 1.330000 now iterating at: 18:08:44 rms-change max change #iterations 10.27438 291.8115 at 10iterations 5.903028 134.2388 at 20iterations 3.366584 80.88651 at 30iterations 1.905964 37.82095 at 40iterations 1.072494 26.04844 at 50iterations 0.6029413 13.25113 at 60iterations 0.3374408 7.379364 at 70iterations 0.1886667 3.571152 at 80iterations 0.1051043 1.999531 at 90iterations 5.8641821E-02 1.102927 at 100iterations 3.2685611E-02 0.5950699 at 110iterations 1.8192295E-02 0.3726349 at 120iterations 1.0118794E-02 0.1767120 at 130iterations 5.6316950E-03 0.1051254 at 140iterations 3.1403997E-03 6.1082363E-02 at 150iterations 1.7553923E-03 3.1764984E-02 at 160iterations 9.8823255E-04 1.7621994E-02 at 170iterations 5.6096551E-04 1.0337830E-02 at 180iterations finished qdiffx linear iterations at : 18:08:57 total time elapsed so far: 13.67000 # loops : 180 mean,max change (kT/e) : 5.6096551E-04 1.0337830E-02 energy calculations done at 13.67000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.80000 DelPhi exited at 18:08:57 13.800u 0.234s 0:14.33 97.9% 0+0k 0+0io 0pf+0w