Tue Oct 11 03:36:03 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 03:36:03 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2196 !!! WARNING: HIR 435 has a net charge of 0.5140 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: 0.6344680 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): -1.707000 46.67100 ymin,ymax (A): -15.91100 32.81400 zmin,zma (A): 39.28200 95.39200 x,y,z range (A): 48.37800 48.72500 56.11000 scale (grids/A): 0.6344680 object centre (A): 22.48200 8.451500 67.33700 number of atom coordinates read : 2196 total number of charged atoms : 2064 net assigned charge : -5.985983 assigned positive charge : 318.5074 centred at (gu) : 89.51932 89.32992 89.18775 assigned negative charge : -324.4938 centred at (gu) : 89.55842 89.51430 89.20821 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5701 nv = 96 ne = 84 npr = 46900 no. pairs analyzed = 46900 no. exposed pairs = 2826 no. arc points = 19801 no. surface atoms = 956 nbur = 1240 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 295 mr = 2919 m= 2 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 25 time to turn everything in is 0.2900000 number of dielectric boundary points 3043 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1886 ## 158 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7030 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.9039143E-09 -7.8166478E-09 midg,1,midg; midg,igrid,midg 8.8549861E-09 -2.0171683E-08 1,midg,midg; igrid,midg,midg -4.7230544E-09 -9.7910853E-09 gauss-seidel spectral radius is 0.9870960 estimated iterations to convergence 72 setup time was (sec) 0.5200000 now iterating at: 03:36:04 rms-change max change #iterations 0.1309044 20.59193 at 10iterations 1.2557136E-02 2.190795 at 20iterations 1.1765009E-03 0.1682053 at 30iterations 1.1542437E-04 1.7837524E-02 at 40iterations 1.1434015E-05 1.8367767E-03 at 50iterations finished qdiffx linear iterations at : 03:36:06 total time elapsed so far: 3.180000 # loops : 50 mean,max change (kT/e) : 1.1434015E-05 1.8367767E-03 energy calculations done at 3.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 03:36:07 3.373u 0.178s 0:03.98 88.9% 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 Tue Oct 11 2011 at 03:36:07 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2196 !!! WARNING: HIR 435 has a net charge of 0.5140 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: 1.903404 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): -1.707000 46.67100 ymin,ymax (A): -15.91100 32.81400 zmin,zma (A): 39.28200 95.39200 x,y,z range (A): 48.37800 48.72500 56.11000 scale (grids/A): 1.903404 object centre (A): 22.48200 8.451500 67.33700 number of atom coordinates read : 2196 total number of charged atoms : 2064 net assigned charge : -5.985983 assigned positive charge : 318.5074 centred at (gu) : 88.55760 87.98940 87.56270 assigned negative charge : -324.4938 centred at (gu) : 88.67524 88.54275 87.62457 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 61212 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19801 grid for indexing accessible points = 1.400000 m= 21214 mr = 40677 m= 3332 mr = 15088 m= 185 mr = 1933 m= 3 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 920 time to turn everything in is 0.5000000 number of dielectric boundary points 28197 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 111 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 16243 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) : 0.6344680 object centre at (A) : 22.48200 8.451500 67.33700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3228460E-03 -2.8265113E-02 midg,1,midg; midg,igrid,midg 1.4593834E-02 -3.7899114E-02 1,midg,midg; igrid,midg,midg -1.6260094E-03 -1.3446344E-02 gauss-seidel spectral radius is 0.9985918 estimated iterations to convergence 211 setup time was (sec) 0.7800000 now iterating at: 03:36:08 rms-change max change #iterations 3.811014 164.6053 at 10iterations 1.757105 66.83608 at 20iterations 0.8124571 30.72327 at 30iterations 0.3760388 13.55825 at 40iterations 0.1743323 6.251160 at 50iterations 8.0502599E-02 2.623916 at 60iterations 3.7247121E-02 1.273389 at 70iterations 1.7240554E-02 0.5469418 at 80iterations 7.9629300E-03 0.2794647 at 90iterations 3.6764743E-03 0.1200027 at 100iterations 1.7037268E-03 5.7113647E-02 at 110iterations 7.8785646E-04 2.7053833E-02 at 120iterations finished qdiffx linear iterations at : 03:36:15 total time elapsed so far: 7.260000 # loops : 120 mean,max change (kT/e) : 7.8785646E-04 2.7053833E-02 energy calculations done at 7.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.440000 DelPhi exited at 03:36:15 7.445u 0.202s 0:08.13 93.9% 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 Tue Oct 11 2011 at 03:36:15 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2196 !!! WARNING: HIR 435 has a net charge of 0.5140 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: 2.855106 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): -1.707000 46.67100 ymin,ymax (A): -15.91100 32.81400 zmin,zma (A): 39.28200 95.39200 x,y,z range (A): 48.37800 48.72500 56.11000 scale (grids/A): 2.855106 object centre (A): 22.48200 8.451500 67.33700 number of atom coordinates read : 2196 total number of charged atoms : 2064 net assigned charge : -5.985983 assigned positive charge : 318.5074 centred at (gu) : 87.83633 86.98402 86.34413 assigned negative charge : -324.4938 centred at (gu) : 88.01289 87.81412 86.43687 start vw surface at 0.1500000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 141460 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19801 grid for indexing accessible points = 1.400000 m= 68233 mr = 99214 m= 24858 mr = 54282 m= 5922 mr = 19434 m= 786 mr = 4179 m= 40 mr = 510 m= 0 mr = 7 time to grow re-entrant surface = 0.6800001 no. cavity mid-points inaccessible to solvent = 2979 time to turn everything in is 1.220000 number of dielectric boundary points 63673 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 16512 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) : 1.903404 object centre at (A) : 22.48200 8.451500 67.33700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1724263E-02 -0.2381311 midg,1,midg; midg,igrid,midg 0.2425842 -0.3612469 1,midg,midg; igrid,midg,midg 0.1011671 -9.5054843E-02 gauss-seidel spectral radius is 0.9992432 estimated iterations to convergence 287 setup time was (sec) 1.520000 now iterating at: 03:36:17 rms-change max change #iterations 8.922112 400.8895 at 10iterations 5.123225 121.7704 at 20iterations 2.929932 59.74792 at 30iterations 1.672355 38.39404 at 40iterations 0.9530960 20.03120 at 50iterations 0.5433560 10.90831 at 60iterations 0.3095512 6.026148 at 70iterations 0.1765162 3.644644 at 80iterations 0.1004331 1.987755 at 90iterations 5.7176899E-02 1.142426 at 100iterations 3.2584231E-02 0.6504421 at 110iterations 1.8553184E-02 0.3895378 at 120iterations 1.0585794E-02 0.2032356 at 130iterations 6.0095838E-03 0.1234627 at 140iterations 3.4339880E-03 7.3774338E-02 at 150iterations 1.9577839E-03 3.8433075E-02 at 160iterations 1.1163536E-03 2.1365643E-02 at 170iterations 6.3784607E-04 1.2809753E-02 at 180iterations finished qdiffx linear iterations at : 03:36:27 total time elapsed so far: 11.88000 # loops : 180 mean,max change (kT/e) : 6.3784607E-04 1.2809753E-02 energy calculations done at 11.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.07000 DelPhi exited at 03:36:28 12.073u 0.195s 0:12.58 97.4% 0+0k 0+0io 0pf+0w