Sun Oct 9 08:16:47 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 08:16:48 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4893 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5206886 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): 46.50600 114.8770 ymin,ymax (A): 40.33900 105.1660 zmin,zma (A): 70.77200 132.5430 x,y,z range (A): 68.37100 64.82700 61.77100 scale (grids/A): 0.5206886 object centre (A): 80.69150 72.75250 101.6575 number of atom coordinates read : 4893 total number of charged atoms : 4733 net assigned charge : -2.999991 assigned positive charge : 744.5208 centred at (gu) : 91.15180 91.54382 89.59263 assigned negative charge : -747.5264 centred at (gu) : 91.23563 91.55520 89.52052 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8433 nv = 96 ne = 84 npr = 97880 no. pairs analyzed = 97880 no. exposed pairs = 6242 no. arc points = 43355 no. surface atoms = 2101 nbur = 2792 mkacc time = 0.2100000 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= 303 mr = 4292 m= 0 mr = 7 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.4600000 number of dielectric boundary points 4437 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4337 ## 639 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 11291 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.9973333E-10 2.1135663E-10 midg,1,midg; midg,igrid,midg -8.9730931E-12 -1.5805030E-10 1,midg,midg; igrid,midg,midg 2.0876380E-10 -5.5326682E-10 gauss-seidel spectral radius is 0.9811451 estimated iterations to convergence 60 setup time was (sec) 0.6700000 now iterating at: 08:16:48 rms-change max change #iterations 7.5486116E-02 10.07530 at 10iterations 5.0289324E-03 0.7741642 at 20iterations 6.5867801E-04 0.1717758 at 30iterations 1.9019496E-04 5.0552368E-02 at 40iterations 6.2178769E-05 1.5628815E-02 at 50iterations finished qdiffx linear iterations at : 08:16:51 total time elapsed so far: 3.080000 # loops : 50 mean,max change (kT/e) : 6.2178769E-05 1.5628815E-02 energy calculations done at 3.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.250000 DelPhi exited at 08:16:51 3.250u 0.143s 0:03.68 92.1% 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 08:16:51 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 = 4893 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.562066 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): 46.50600 114.8770 ymin,ymax (A): 40.33900 105.1660 zmin,zma (A): 70.77200 132.5430 x,y,z range (A): 68.37100 64.82700 61.77100 scale (grids/A): 1.562066 object centre (A): 80.69150 72.75250 101.6575 number of atom coordinates read : 4893 total number of charged atoms : 4733 net assigned charge : -2.999991 assigned positive charge : 744.5208 centred at (gu) : 93.45361 94.62983 88.77579 assigned negative charge : -747.5264 centred at (gu) : 93.70641 94.66515 88.56107 start vw surface at 0.1800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 93890 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43355 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 27808 mr = 63458 m= 2645 mr = 18556 m= 62 mr = 1311 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 526 time to turn everything in is 0.6200000 number of dielectric boundary points 41080 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 623 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 35839 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) : 0.5206886 object centre at (A) : 80.69150 72.75250 101.6575 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.9594979E-03 -4.6213372E-03 midg,1,midg; midg,igrid,midg -6.5482347E-03 -2.3886929E-03 1,midg,midg; igrid,midg,midg 9.8080165E-04 -1.0088068E-02 gauss-seidel spectral radius is 0.9982123 estimated iterations to convergence 188 setup time was (sec) 0.8800000 now iterating at: 08:16:52 rms-change max change #iterations 4.053136 176.0399 at 10iterations 1.703064 57.18762 at 20iterations 0.7161146 27.42448 at 30iterations 0.3002225 10.29655 at 40iterations 0.1266942 4.265276 at 50iterations 5.3280603E-02 1.664130 at 60iterations 2.2510840E-02 0.6948166 at 70iterations 9.4763897E-03 0.2922756 at 80iterations 4.0102559E-03 0.1172028 at 90iterations 1.7100129E-03 5.7277679E-02 at 100iterations 7.3751417E-04 2.4940491E-02 at 110iterations 3.2730281E-04 1.1302948E-02 at 120iterations finished qdiffx linear iterations at : 08:16:58 total time elapsed so far: 6.910000 # loops : 120 mean,max change (kT/e) : 3.2730281E-04 1.1302948E-02 energy calculations done at 6.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.090000 DelPhi exited at 08:16:59 7.092u 0.169s 0:07.54 96.1% 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 08:16:59 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4893 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 2.343099 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): 46.50600 114.8770 ymin,ymax (A): 40.33900 105.1660 zmin,zma (A): 70.77200 132.5430 x,y,z range (A): 68.37100 64.82700 61.77100 scale (grids/A): 2.343099 object centre (A): 80.69150 72.75250 101.6575 number of atom coordinates read : 4893 total number of charged atoms : 4733 net assigned charge : -2.999991 assigned positive charge : 744.5208 centred at (gu) : 95.17970 96.94433 88.16337 assigned negative charge : -747.5264 centred at (gu) : 95.55954 96.99744 87.84140 start vw surface at 0.2000000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 218518 reading accessible surface arcs data from file ARCDAT no. of arc points read = 43355 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 97750 mr = 156178 m= 26298 mr = 75524 m= 4022 mr = 19538 m= 212 mr = 2646 m= 4 mr = 94 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 1786 time to turn everything in is 1.530000 number of dielectric boundary points 92824 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 53 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 37771 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) : 1.562066 object centre at (A) : 80.69150 72.75250 101.6575 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2300429 -0.2444132 midg,1,midg; midg,igrid,midg -0.1218427 -0.1254870 1,midg,midg; igrid,midg,midg 3.8277980E-02 -9.3203709E-03 gauss-seidel spectral radius is 0.9992063 estimated iterations to convergence 280 setup time was (sec) 1.810000 now iterating at: 08:17:01 rms-change max change #iterations 11.01246 314.0418 at 10iterations 6.471429 157.7982 at 20iterations 3.759530 78.54610 at 30iterations 2.177296 48.62004 at 40iterations 1.252116 26.98088 at 50iterations 0.7195495 15.11475 at 60iterations 0.4119591 8.051941 at 70iterations 0.2349055 4.487048 at 80iterations 0.1336722 2.609543 at 90iterations 7.5924426E-02 1.460312 at 100iterations 4.3093145E-02 0.7782698 at 110iterations 2.4496645E-02 0.4631901 at 120iterations 1.3883219E-02 0.2493896 at 130iterations 7.8679333E-03 0.1568184 at 140iterations 4.4657737E-03 8.4945679E-02 at 150iterations 2.5279932E-03 5.0684035E-02 at 160iterations 1.4381072E-03 2.5890350E-02 at 170iterations 8.1898860E-04 1.4278412E-02 at 180iterations finished qdiffx linear iterations at : 08:17:10 total time elapsed so far: 11.38000 # loops : 180 mean,max change (kT/e) : 8.1898860E-04 1.4278412E-02 energy calculations done at 11.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.55000 DelPhi exited at 08:17:11 11.555u 0.169s 0:12.01 97.5% 0+0k 0+0io 0pf+0w