Tue Nov 22 14:09:32 PST 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 Nov 22 2011 at 14:09:33 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 0.6431449 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): -6.004000 34.41700 ymin,ymax (A): -3.598000 47.72800 zmin,zma (A): -24.34800 31.00500 x,y,z range (A): 40.42100 51.32600 55.35300 scale (grids/A): 0.6431449 object centre (A): 14.20650 22.06500 3.328501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.4260 centred at (gu) : 90.79190 92.61972 90.15471 assigned negative charge : -288.4263 centred at (gu) : 90.89828 92.74712 90.10717 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 5496 nv = 96 ne = 84 npr = 41204 no. pairs analyzed = 41204 no. exposed pairs = 2403 no. arc points = 16977 no. surface atoms = 814 nbur = 1150 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 264 mr = 3093 m= 0 mr = 35 time to grow re-entrant surface = 7.0000000E-02 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.1600000 number of dielectric boundary points 2632 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1704 ## 177 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 6532 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.0244388E-10 9.9287014E-09 midg,1,midg; midg,igrid,midg 9.7580060E-09 -1.2573467E-08 1,midg,midg; igrid,midg,midg 1.2694670E-08 -5.8526162E-09 gauss-seidel spectral radius is 0.9874155 estimated iterations to convergence 73 setup time was (sec) 0.3700000 now iterating at: 14:09:33 rms-change max change #iterations 0.1304768 20.26558 at 10iterations 1.3063097E-02 2.294496 at 20iterations 1.2780292E-03 0.2233200 at 30iterations 1.3055628E-04 1.9767761E-02 at 40iterations 1.2782686E-05 2.0580292E-03 at 50iterations finished qdiffx linear iterations at : 14:09:36 total time elapsed so far: 3.450000 # loops : 50 mean,max change (kT/e) : 1.2782686E-05 2.0580292E-03 energy calculations done at 3.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.580000 DelPhi exited at 14:09:37 3.584u 0.215s 0:04.16 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 Tue Nov 22 2011 at 14:09:37 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 1.929435 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): -6.004000 34.41700 ymin,ymax (A): -3.598000 47.72800 zmin,zma (A): -24.34800 31.00500 x,y,z range (A): 40.42100 51.32600 55.35300 scale (grids/A): 1.929435 object centre (A): 14.20650 22.06500 3.328501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.4260 centred at (gu) : 92.37541 97.85907 90.46407 assigned negative charge : -288.4263 centred at (gu) : 92.69505 98.24138 90.32146 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 58926 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16977 grid for indexing accessible points = 1.400000 m= 21415 mr = 40922 m= 3114 mr = 16209 m= 137 mr = 1955 m= 2 mr = 51 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 1229 time to turn everything in is 0.3200000 number of dielectric boundary points 24457 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 127 iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 14415 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) : 0.6431449 object centre at (A) : 14.20650 22.06500 3.328501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.4526733E-02 1.3024504E-02 midg,1,midg; midg,igrid,midg 2.9230477E-02 -6.8726111E-03 1,midg,midg; igrid,midg,midg 8.8341124E-03 -4.4716736E-03 gauss-seidel spectral radius is 0.9985881 estimated iterations to convergence 211 setup time was (sec) 0.5500000 now iterating at: 14:09:38 rms-change max change #iterations 3.714433 166.3092 at 10iterations 1.718637 62.83791 at 20iterations 0.7949092 28.84942 at 30iterations 0.3688197 13.13659 at 40iterations 0.1705895 5.761620 at 50iterations 7.8340366E-02 2.990093 at 60iterations 3.6207300E-02 1.197332 at 70iterations 1.6748313E-02 0.6055450 at 80iterations 7.7425721E-03 0.2748032 at 90iterations 3.5948928E-03 0.1221182 at 100iterations 1.6534603E-03 5.7247162E-02 at 110iterations 7.6664926E-04 3.0700684E-02 at 120iterations finished qdiffx linear iterations at : 14:09:45 total time elapsed so far: 8.150000 # loops : 120 mean,max change (kT/e) : 7.6664926E-04 3.0700684E-02 energy calculations done at 8.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.280000 DelPhi exited at 14:09:46 8.282u 0.264s 0:08.88 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 Tue Nov 22 2011 at 14:09:46 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: 265 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 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: 2.894152 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): -6.004000 34.41700 ymin,ymax (A): -3.598000 47.72800 zmin,zma (A): -24.34800 31.00500 x,y,z range (A): 40.42100 51.32600 55.35300 scale (grids/A): 2.894152 object centre (A): 14.20650 22.06500 3.328501 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 291.4260 centred at (gu) : 93.56308 101.7885 90.69616 assigned negative charge : -288.4263 centred at (gu) : 94.04269 102.3621 90.48235 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 136197 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16977 grid for indexing accessible points = 1.400000 m= 69141 mr = 98777 m= 25123 mr = 57290 m= 5536 mr = 20800 m= 688 mr = 4190 m= 42 mr = 443 m= 2 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 4314 time to turn everything in is 0.7900000 number of dielectric boundary points 55213 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 14654 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) : 1.929435 object centre at (A) : 14.20650 22.06500 3.328501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.075999 2.2421919E-02 midg,1,midg; midg,igrid,midg 0.2987344 -0.1069686 1,midg,midg; igrid,midg,midg 4.9262203E-02 -2.5424296E-02 gauss-seidel spectral radius is 0.9992304 estimated iterations to convergence 285 setup time was (sec) 1.020000 now iterating at: 14:09:47 rms-change max change #iterations 8.630797 347.4839 at 10iterations 4.937798 113.8050 at 20iterations 2.795376 59.79918 at 30iterations 1.586261 31.61896 at 40iterations 0.8993167 18.44928 at 50iterations 0.5099795 9.952357 at 60iterations 0.2884669 6.157806 at 70iterations 0.1638178 3.793814 at 80iterations 9.2855439E-02 1.848678 at 90iterations 5.2667182E-02 1.147236 at 100iterations 2.9868368E-02 0.6379795 at 110iterations 1.6879046E-02 0.3467445 at 120iterations 9.5937438E-03 0.2028511 at 130iterations 5.4278048E-03 0.1080408 at 140iterations 3.0820735E-03 6.9599152E-02 at 150iterations 1.7481616E-03 3.4940720E-02 at 160iterations 9.8930090E-04 1.8731117E-02 at 170iterations 5.6176243E-04 1.2767792E-02 at 180iterations finished qdiffx linear iterations at : 14:09:59 total time elapsed so far: 13.01000 # loops : 180 mean,max change (kT/e) : 5.6176243E-04 1.2767792E-02 energy calculations done at 13.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.15000 DelPhi exited at 14:09:59 13.151u 0.256s 0:13.69 97.8% 0+0k 0+0io 0pf+0w