Mon Oct 10 13:59:48 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 Mon Oct 10 2011 at 13:59:48 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4234 !!! WARNING: HIR 440 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5885659 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): -25.06100 35.42500 ymin,ymax (A): 35.36100 93.06100 zmin,zma (A): 31.09800 90.66300 x,y,z range (A): 60.48600 57.70000 59.56500 scale (grids/A): 0.5885659 object centre (A): 5.182000 64.21100 60.88050 number of atom coordinates read : 4234 total number of charged atoms : 4087 net assigned charge : -0.9859604 assigned positive charge : 638.7515 centred at (gu) : 90.90832 89.53159 88.49610 assigned negative charge : -639.7405 centred at (gu) : 90.74868 89.66071 88.69170 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 9566 nv = 96 ne = 84 npr = 88073 no. pairs analyzed = 88073 no. exposed pairs = 4862 no. arc points = 32881 no. surface atoms = 1649 nbur = 2585 mkacc time = 0.2300000 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 = 1.456000 m= 462 mr = 5607 m= 2 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 114 time to turn everything in is 0.4700000 number of dielectric boundary points 4384 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3487 ## 380 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 12415 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0709863E-08 -6.2522689E-09 midg,1,midg; midg,igrid,midg 5.3783924E-09 -5.3655831E-09 1,midg,midg; igrid,midg,midg -5.9101910E-09 7.5007547E-09 gauss-seidel spectral radius is 0.9851905 estimated iterations to convergence 67 setup time was (sec) 0.7500000 now iterating at: 13:59:49 rms-change max change #iterations 0.1291296 20.31318 at 10iterations 1.0992846E-02 1.414192 at 20iterations 1.2191535E-03 0.1581841 at 30iterations 2.7186837E-04 3.3535004E-02 at 40iterations 9.1586851E-05 1.1011839E-02 at 50iterations finished qdiffx linear iterations at : 13:59:53 total time elapsed so far: 4.570000 # loops : 50 mean,max change (kT/e) : 9.1586851E-05 1.1011839E-02 energy calculations done at 4.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.730000 DelPhi exited at 13:59:54 4.734u 0.394s 0:05.92 86.4% 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 Mon Oct 10 2011 at 13:59:54 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4234 !!! WARNING: HIR 440 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.765698 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): -25.06100 35.42500 ymin,ymax (A): 35.36100 93.06100 zmin,zma (A): 31.09800 90.66300 x,y,z range (A): 60.48600 57.70000 59.56500 scale (grids/A): 1.765698 object centre (A): 5.182000 64.21100 60.88050 number of atom coordinates read : 4234 total number of charged atoms : 4087 net assigned charge : -0.9859604 assigned positive charge : 638.7515 centred at (gu) : 92.72362 88.59331 85.48704 assigned negative charge : -639.7405 centred at (gu) : 92.24575 88.98149 86.07476 start vw surface at 0.1500000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 106047 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32881 grid for indexing accessible points = 1.400000 m= 38523 mr = 77369 m= 5503 mr = 28995 m= 268 mr = 3509 m= 5 mr = 65 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 4310 time to turn everything in is 0.8300000 number of dielectric boundary points 40408 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 327 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 31797 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) : 0.5885659 object centre at (A) : 5.182000 64.21100 60.88050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.6298969E-02 -3.5152260E-02 midg,1,midg; midg,igrid,midg 2.6214538E-02 -2.9268719E-02 1,midg,midg; igrid,midg,midg -2.3485811E-02 4.4259593E-02 gauss-seidel spectral radius is 0.9985647 estimated iterations to convergence 209 setup time was (sec) 1.150000 now iterating at: 13:59:55 rms-change max change #iterations 4.879771 197.5613 at 10iterations 2.231853 63.77866 at 20iterations 1.026636 29.03949 at 30iterations 0.4732124 12.41773 at 40iterations 0.2174897 5.745785 at 50iterations 9.9993698E-02 2.780787 at 60iterations 4.6194900E-02 1.206460 at 70iterations 2.1307433E-02 0.6012239 at 80iterations 9.8836245E-03 0.2542820 at 90iterations 4.6036723E-03 0.1242037 at 100iterations 2.1880795E-03 6.2747955E-02 at 110iterations 1.0689814E-03 2.9842377E-02 at 120iterations finished qdiffx linear iterations at : 14:00:06 total time elapsed so far: 11.41000 # loops : 120 mean,max change (kT/e) : 1.0689814E-03 2.9842377E-02 energy calculations done at 11.41000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.57000 DelPhi exited at 14:00:06 11.575u 0.468s 0:12.56 95.7% 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 Mon Oct 10 2011 at 14:00:07 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4234 !!! WARNING: HIR 440 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.648547 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): -25.06100 35.42500 ymin,ymax (A): 35.36100 93.06100 zmin,zma (A): 31.09800 90.66300 x,y,z range (A): 60.48600 57.70000 59.56500 scale (grids/A): 2.648547 object centre (A): 5.182000 64.21100 60.88050 number of atom coordinates read : 4234 total number of charged atoms : 4087 net assigned charge : -0.9859604 assigned positive charge : 638.7515 centred at (gu) : 94.08524 87.88978 83.23016 assigned negative charge : -639.7405 centred at (gu) : 93.36843 88.47218 84.11198 start vw surface at 0.1600000 fill in re-entrant regions at 0.6900000 boundary points on vw surface= 246639 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32881 grid for indexing accessible points = 1.400000 m= 127336 mr = 187699 m= 43730 mr = 105997 m= 9767 mr = 35512 m= 1148 mr = 7483 m= 36 mr = 735 m= 0 mr = 2 time to grow re-entrant surface = 1.420000 no. cavity mid-points inaccessible to solvent = 14125 time to turn everything in is 2.260000 number of dielectric boundary points 91228 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 2.420000 number of grid points assigned charge 32688 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) : 1.765698 object centre at (A) : 5.182000 64.21100 60.88050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.031552 -0.4105177 midg,1,midg; midg,igrid,midg 0.3331067 -0.3441623 1,midg,midg; igrid,midg,midg -0.2217895 0.3413520 gauss-seidel spectral radius is 0.9992670 estimated iterations to convergence 291 setup time was (sec) 2.630000 now iterating at: 14:00:10 rms-change max change #iterations 11.85619 316.3852 at 10iterations 7.027249 159.1055 at 20iterations 4.125951 101.7147 at 30iterations 2.411164 46.97215 at 40iterations 1.408789 23.52498 at 50iterations 0.8176973 13.37326 at 60iterations 0.4737472 7.378991 at 70iterations 0.2751786 4.316513 at 80iterations 0.1592522 2.658298 at 90iterations 9.2268646E-02 1.477901 at 100iterations 5.3458460E-02 0.8803449 at 110iterations 3.0921830E-02 0.5096405 at 120iterations 1.7910672E-02 0.3056202 at 130iterations 1.0350880E-02 0.1685944 at 140iterations 6.0396311E-03 8.9613914E-02 at 150iterations 3.5427411E-03 5.8380127E-02 at 160iterations 2.1008139E-03 3.5670757E-02 at 170iterations 1.2733840E-03 2.1041870E-02 at 180iterations finished qdiffx linear iterations at : 14:00:28 total time elapsed so far: 20.53000 # loops : 180 mean,max change (kT/e) : 1.2733840E-03 2.1041870E-02 energy calculations done at 20.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.68000 DelPhi exited at 14:00:29 20.686u 0.492s 0:21.79 97.1% 0+0k 0+0io 0pf+0w