Tue Oct 11 05:29:56 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 Tue Oct 11 2011 at 05:29:56 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 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: 0.6782761 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): 1.644000 46.71900 ymin,ymax (A): 0.5100001 41.57700 zmin,zma (A): -2.548000 49.93800 x,y,z range (A): 45.07500 41.06700 52.48600 scale (grids/A): 0.6782761 object centre (A): 24.18150 21.04350 23.69500 number of atom coordinates read : 2290 total number of charged atoms : 1969 net assigned charge : 6.500009 assigned positive charge : 319.1440 centred at (gu) : 90.64743 90.28642 89.65884 assigned negative charge : -312.6442 centred at (gu) : 90.77505 90.28349 89.72719 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6513 nv = 96 ne = 84 npr = 41971 no. pairs analyzed = 41971 no. exposed pairs = 2580 no. arc points = 17407 no. surface atoms = 879 nbur = 1411 mkacc time = 8.9999989E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 416 mr = 3745 m= 5 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3134 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1711 ## 145 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7466 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.7102894E-08 9.0726253E-09 midg,1,midg; midg,igrid,midg 2.4772918E-08 2.9263585E-08 1,midg,midg; igrid,midg,midg 5.1434991E-08 -6.6180981E-09 gauss-seidel spectral radius is 0.9886786 estimated iterations to convergence 77 setup time was (sec) 0.4900000 now iterating at: 05:29:57 rms-change max change #iterations 0.1685324 25.68253 at 10iterations 1.9210851E-02 3.163471 at 20iterations 2.4311079E-03 0.3429852 at 30iterations 4.1345839E-04 5.2642822E-02 at 40iterations 1.0567711E-04 1.2638092E-02 at 50iterations finished qdiffx linear iterations at : 05:29:59 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 1.0567711E-04 1.2638092E-02 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 05:30:00 3.354u 0.216s 0:03.85 92.4% 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 Tue Oct 11 2011 at 05:30:00 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 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: 2.034828 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): 1.644000 46.71900 ymin,ymax (A): 0.5100001 41.57700 zmin,zma (A): -2.548000 49.93800 x,y,z range (A): 45.07500 41.06700 52.48600 scale (grids/A): 2.034828 object centre (A): 24.18150 21.04350 23.69500 number of atom coordinates read : 2290 total number of charged atoms : 1969 net assigned charge : 6.500009 assigned positive charge : 319.1440 centred at (gu) : 91.94239 90.85906 88.97626 assigned negative charge : -312.6442 centred at (gu) : 92.32520 90.85051 89.18169 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 69231 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17407 grid for indexing accessible points = 1.400000 m= 27259 mr = 49188 m= 4878 mr = 20581 m= 380 mr = 3145 m= 16 mr = 164 m= 0 mr = 2 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5300000 number of dielectric boundary points 28684 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 93 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 15558 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) : 0.6782761 object centre at (A) : 24.18150 21.04350 23.69500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8666026E-02 5.2099545E-02 midg,1,midg; midg,igrid,midg 4.6988726E-03 2.2428373E-02 1,midg,midg; igrid,midg,midg 2.7025454E-02 -1.1506859E-03 gauss-seidel spectral radius is 0.9987404 estimated iterations to convergence 223 setup time was (sec) 0.8100000 now iterating at: 05:30:01 rms-change max change #iterations 4.258427 195.2404 at 10iterations 2.064183 67.11698 at 20iterations 1.000175 34.35387 at 30iterations 0.4811286 15.84876 at 40iterations 0.2335881 7.658762 at 50iterations 0.1131385 3.635099 at 60iterations 5.4758128E-02 1.900341 at 70iterations 2.6568312E-02 0.8319340 at 80iterations 1.2964313E-02 0.3891001 at 90iterations 6.3556000E-03 0.1933222 at 100iterations 3.1430831E-03 0.1006622 at 110iterations 1.6073617E-03 4.8721313E-02 at 120iterations finished qdiffx linear iterations at : 05:30:07 total time elapsed so far: 7.320000 # loops : 120 mean,max change (kT/e) : 1.6073617E-03 4.8721313E-02 energy calculations done at 7.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.500000 DelPhi exited at 05:30:08 7.499u 0.223s 0:08.09 95.3% 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 Tue Oct 11 2011 at 05:30:08 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2290 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: 3.052243 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): 1.644000 46.71900 ymin,ymax (A): 0.5100001 41.57700 zmin,zma (A): -2.548000 49.93800 x,y,z range (A): 45.07500 41.06700 52.48600 scale (grids/A): 3.052243 object centre (A): 24.18150 21.04350 23.69500 number of atom coordinates read : 2290 total number of charged atoms : 1969 net assigned charge : 6.500009 assigned positive charge : 319.1440 centred at (gu) : 92.91356 91.28867 88.46442 assigned negative charge : -312.6442 centred at (gu) : 93.48788 91.27583 88.77258 start vw surface at 0.1500000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 159663 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17407 grid for indexing accessible points = 1.400000 m= 86006 mr = 118465 m= 33634 mr = 71476 m= 9023 mr = 27553 m= 1566 mr = 6822 m= 141 mr = 1057 m= 1 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.330000 number of dielectric boundary points 64594 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.460000 number of grid points assigned charge 15752 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) : 2.034828 object centre at (A) : 24.18150 21.04350 23.69500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3931074 0.7676228 midg,1,midg; midg,igrid,midg 1.4654825E-02 0.2005996 1,midg,midg; igrid,midg,midg 0.2358489 3.4862291E-02 gauss-seidel spectral radius is 0.9992726 estimated iterations to convergence 293 setup time was (sec) 1.630000 now iterating at: 05:30:10 rms-change max change #iterations 9.739190 323.4901 at 10iterations 5.726462 178.6659 at 20iterations 3.367538 74.81803 at 30iterations 1.969493 38.80666 at 40iterations 1.145877 24.29644 at 50iterations 0.6698007 15.26491 at 60iterations 0.3898740 8.300282 at 70iterations 0.2269483 5.045071 at 80iterations 0.1317571 2.509789 at 90iterations 7.6579548E-02 1.397873 at 100iterations 4.4643044E-02 0.8316206 at 110iterations 2.6067208E-02 0.5466614 at 120iterations 1.5253471E-02 0.2985945 at 130iterations 9.0475911E-03 0.1649628 at 140iterations 5.4536317E-03 0.1016464 at 150iterations 3.4051752E-03 7.8582764E-02 at 160iterations 2.2342841E-03 4.2106628E-02 at 170iterations 1.5519470E-03 2.7862549E-02 at 180iterations finished qdiffx linear iterations at : 05:30:20 total time elapsed so far: 12.02000 # loops : 180 mean,max change (kT/e) : 1.5519470E-03 2.7862549E-02 energy calculations done at 12.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.20000 DelPhi exited at 05:30:21 12.207u 0.242s 0:13.07 95.1% 0+0k 0+0io 0pf+0w