Mon Oct 10 14:15:46 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 Mon Oct 10 2011 at 14:15:46 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 = 2160 !!! WARNING: MG3 318 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7358260 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): 15.05800 54.48400 ymin,ymax (A): -7.529000 40.85200 zmin,zma (A): -5.098000 38.51800 x,y,z range (A): 39.42599 48.38100 43.61600 scale (grids/A): 0.7358260 object centre (A): 34.77100 16.66150 16.71000 number of atom coordinates read : 2160 total number of charged atoms : 2028 net assigned charge : -2.599991 assigned positive charge : 323.1287 centred at (gu) : 89.10447 90.56114 89.11421 assigned negative charge : -325.7290 centred at (gu) : 89.09401 90.54479 89.10996 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7718 nv = 96 ne = 84 npr = 46219 no. pairs analyzed = 46219 no. exposed pairs = 2484 no. arc points = 16721 no. surface atoms = 850 nbur = 1310 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 582 mr = 4630 m= 2 mr = 138 m= 0 mr = 0 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 212 time to turn everything in is 0.1800000 number of dielectric boundary points 3534 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1415 ## 106 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8628 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.3826568E-08 -3.2192105E-08 midg,1,midg; midg,igrid,midg -5.1652830E-08 -2.8976066E-08 1,midg,midg; igrid,midg,midg -6.0936379E-08 -2.7185935E-08 gauss-seidel spectral radius is 0.9903698 estimated iterations to convergence 83 setup time was (sec) 0.3600000 now iterating at: 14:15:46 rms-change max change #iterations 0.2407425 41.50147 at 10iterations 3.2047592E-02 4.417666 at 20iterations 4.3318113E-03 0.5333252 at 30iterations 5.7175040E-04 7.7079058E-02 at 40iterations 7.7068209E-05 9.8056793E-03 at 50iterations finished qdiffx linear iterations at : 14:15:49 total time elapsed so far: 3.210000 # loops : 50 mean,max change (kT/e) : 7.7068209E-05 9.8056793E-03 energy calculations done at 3.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 14:15:50 3.338u 0.180s 0:03.82 91.8% 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 Mon Oct 10 2011 at 14:15:50 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 = 2160 !!! WARNING: MG3 318 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.207478 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): 15.05800 54.48400 ymin,ymax (A): -7.529000 40.85200 zmin,zma (A): -5.098000 38.51800 x,y,z range (A): 39.42599 48.38100 43.61600 scale (grids/A): 2.207478 object centre (A): 34.77100 16.66150 16.71000 number of atom coordinates read : 2160 total number of charged atoms : 2028 net assigned charge : -2.599991 assigned positive charge : 323.1287 centred at (gu) : 87.31325 91.68329 87.34259 assigned negative charge : -325.7290 centred at (gu) : 87.28203 91.63448 87.33015 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 81843 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16721 grid for indexing accessible points = 1.400000 m= 34294 mr = 59178 m= 7920 mr = 26942 m= 917 mr = 5893 m= 31 mr = 582 m= 0 mr = 7 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 5249 time to turn everything in is 0.4000000 number of dielectric boundary points 32403 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 47 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 16151 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) : 0.7358260 object centre at (A) : 34.77100 16.66150 16.71000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9431691E-02 6.4544375E-03 midg,1,midg; midg,igrid,midg 1.4412819E-03 -2.5957033E-02 1,midg,midg; igrid,midg,midg -1.2036001E-02 -1.2273476E-02 gauss-seidel spectral radius is 0.9989025 estimated iterations to convergence 239 setup time was (sec) 0.6200000 now iterating at: 14:15:50 rms-change max change #iterations 5.079351 209.9646 at 10iterations 2.566751 81.77597 at 20iterations 1.304557 43.37613 at 30iterations 0.6632432 18.24844 at 40iterations 0.3361544 9.542931 at 50iterations 0.1704039 5.425335 at 60iterations 8.6432852E-02 2.736451 at 70iterations 4.3899775E-02 1.189057 at 80iterations 2.2194816E-02 0.5847273 at 90iterations 1.1255942E-02 0.3072087 at 100iterations 5.7123080E-03 0.1597748 at 110iterations 2.8955475E-03 8.1477642E-02 at 120iterations finished qdiffx linear iterations at : 14:15:58 total time elapsed so far: 7.680000 # loops : 120 mean,max change (kT/e) : 2.8955475E-03 8.1477642E-02 energy calculations done at 7.680000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 14:15:58 7.807u 0.210s 0:08.79 91.1% 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 Mon Oct 10 2011 at 14:15:59 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 = 2160 !!! WARNING: MG3 318 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.311217 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): 15.05800 54.48400 ymin,ymax (A): -7.529000 40.85200 zmin,zma (A): -5.098000 38.51800 x,y,z range (A): 39.42599 48.38100 43.61600 scale (grids/A): 3.311217 object centre (A): 34.77100 16.66150 16.71000 number of atom coordinates read : 2160 total number of charged atoms : 2028 net assigned charge : -2.599991 assigned positive charge : 323.1287 centred at (gu) : 85.96985 92.52502 86.01389 assigned negative charge : -325.7290 centred at (gu) : 85.92298 92.45177 85.99521 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 188597 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16721 grid for indexing accessible points = 1.400000 m= 103976 mr = 141813 m= 46926 mr = 88270 m= 15759 mr = 39958 m= 3739 mr = 13079 m= 530 mr = 2996 m= 22 mr = 401 m= 0 mr = 3 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 18140 time to turn everything in is 1.260000 number of dielectric boundary points 73029 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 16224 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) : 2.207478 object centre at (A) : 34.77100 16.66150 16.71000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2800016 0.2158931 midg,1,midg; midg,igrid,midg -0.1554899 -0.3335683 1,midg,midg; igrid,midg,midg -1.7768186E-02 -0.1441054 gauss-seidel spectral radius is 0.9993048 estimated iterations to convergence 299 setup time was (sec) 1.500000 now iterating at: 14:16:00 rms-change max change #iterations 10.95136 259.1207 at 10iterations 6.445612 114.1963 at 20iterations 3.781259 76.37529 at 30iterations 2.221108 38.76983 at 40iterations 1.303474 22.97579 at 50iterations 0.7644818 12.43598 at 60iterations 0.4469979 7.307883 at 70iterations 0.2618237 4.185714 at 80iterations 0.1532151 2.543127 at 90iterations 8.9530699E-02 1.397610 at 100iterations 5.2611347E-02 0.8624835 at 110iterations 3.0743025E-02 0.5364647 at 120iterations 1.8023277E-02 0.3159866 at 130iterations 1.0552119E-02 0.1655598 at 140iterations 6.2048687E-03 0.1014137 at 150iterations 3.6567370E-03 6.1618686E-02 at 160iterations 2.1731253E-03 3.4766197E-02 at 170iterations 1.2981180E-03 2.0567060E-02 at 180iterations finished qdiffx linear iterations at : 14:16:12 total time elapsed so far: 12.88000 # loops : 180 mean,max change (kT/e) : 1.2981180E-03 2.0567060E-02 energy calculations done at 12.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.01000 DelPhi exited at 14:16:12 13.014u 0.205s 0:13.67 96.6% 0+0k 0+0io 0pf+0w