Tue Oct 11 04:31:36 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 04:31:36 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2730 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 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: 0.6527559 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): -11.00100 36.83200 ymin,ymax (A): -26.00200 22.39100 zmin,zma (A): -9.173000 45.36500 x,y,z range (A): 47.83300 48.39300 54.53800 scale (grids/A): 0.6527559 object centre (A): 12.91550 -1.805500 18.09600 number of atom coordinates read : 2730 total number of charged atoms : 2578 net assigned charge : 3.154012 assigned positive charge : 414.4208 centred at (gu) : 89.95441 90.27415 91.54431 assigned negative charge : -411.2673 centred at (gu) : 89.70166 90.10517 91.50137 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 7680 nv = 96 ne = 84 npr = 56044 no. pairs analyzed = 56044 no. exposed pairs = 3276 no. arc points = 22798 no. surface atoms = 1110 nbur = 1620 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 430 mr = 4358 m= 3 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 47 time to turn everything in is 0.4100000 number of dielectric boundary points 3688 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2232 ## 242 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 9203 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.5328937E-10 1.9209548E-08 midg,1,midg; midg,igrid,midg -2.2033008E-08 3.7351612E-08 1,midg,midg; igrid,midg,midg -3.8972658E-08 4.8649298E-08 gauss-seidel spectral radius is 0.9878448 estimated iterations to convergence 74 setup time was (sec) 0.6900000 now iterating at: 04:31:37 rms-change max change #iterations 0.1651585 25.61412 at 10iterations 1.7404007E-02 2.259066 at 20iterations 1.9081632E-03 0.2770729 at 30iterations 2.2956480E-04 3.0330658E-02 at 40iterations 4.0402276E-05 5.4931641E-03 at 50iterations finished qdiffx linear iterations at : 04:31:40 total time elapsed so far: 3.820000 # loops : 50 mean,max change (kT/e) : 4.0402276E-05 5.4931641E-03 energy calculations done at 3.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.050000 DelPhi exited at 04:31:41 4.049u 0.178s 0:04.77 88.2% 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 04:31:41 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2730 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.958268 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): -11.00100 36.83200 ymin,ymax (A): -26.00200 22.39100 zmin,zma (A): -9.173000 45.36500 x,y,z range (A): 47.83300 48.39300 54.53800 scale (grids/A): 1.958268 object centre (A): 12.91550 -1.805500 18.09600 number of atom coordinates read : 2730 total number of charged atoms : 2578 net assigned charge : 3.154012 assigned positive charge : 414.4208 centred at (gu) : 89.86234 90.82161 94.63247 assigned negative charge : -411.2673 centred at (gu) : 89.10471 90.31510 94.50381 start vw surface at 0.1800000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 83355 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22798 grid for indexing accessible points = 1.400000 m= 30937 mr = 59099 m= 4740 mr = 23078 m= 268 mr = 2955 m= 1 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 898 time to turn everything in is 0.7300000 number of dielectric boundary points 34080 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 169 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8800000 number of grid points assigned charge 20340 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) : 0.6527559 object centre at (A) : 12.91550 -1.805500 18.09600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8586676E-02 9.6259182E-03 midg,1,midg; midg,igrid,midg -1.1046560E-02 2.9339418E-02 1,midg,midg; igrid,midg,midg -1.2809359E-02 6.3506953E-02 gauss-seidel spectral radius is 0.9987155 estimated iterations to convergence 221 setup time was (sec) 1.080000 now iterating at: 04:31:42 rms-change max change #iterations 4.654898 191.4642 at 10iterations 2.232903 80.44362 at 20iterations 1.070528 34.12600 at 30iterations 0.5133584 15.83217 at 40iterations 0.2472820 6.881223 at 50iterations 0.1184989 3.183277 at 60iterations 5.6813803E-02 1.948892 at 70iterations 2.7330544E-02 0.7946825 at 80iterations 1.3089447E-02 0.4139500 at 90iterations 6.2892297E-03 0.1892576 at 100iterations 3.0253041E-03 9.0480804E-02 at 110iterations 1.4588902E-03 4.5005798E-02 at 120iterations finished qdiffx linear iterations at : 04:31:50 total time elapsed so far: 8.870000 # loops : 120 mean,max change (kT/e) : 1.4588902E-03 4.5005798E-02 energy calculations done at 8.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.110000 DelPhi exited at 04:31:50 9.112u 0.193s 0:09.77 95.1% 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 Oct 11 2011 at 04:31:50 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2730 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3600 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.937401 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): -11.00100 36.83200 ymin,ymax (A): -26.00200 22.39100 zmin,zma (A): -9.173000 45.36500 x,y,z range (A): 47.83300 48.39300 54.53800 scale (grids/A): 2.937401 object centre (A): 12.91550 -1.805500 18.09600 number of atom coordinates read : 2730 total number of charged atoms : 2578 net assigned charge : 3.154012 assigned positive charge : 414.4208 centred at (gu) : 89.79335 91.23235 96.94848 assigned negative charge : -411.2673 centred at (gu) : 88.65704 90.47262 96.75558 start vw surface at 0.1900000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 192708 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22798 grid for indexing accessible points = 1.400000 m= 99849 mr = 142864 m= 36167 mr = 82491 m= 8609 mr = 29273 m= 1193 mr = 6382 m= 62 mr = 768 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 2912 time to turn everything in is 1.910000 number of dielectric boundary points 76791 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.060000 number of grid points assigned charge 20615 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) : 1.958268 object centre at (A) : 12.91550 -1.805500 18.09600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4452090 0.3675360 midg,1,midg; midg,igrid,midg -0.1205454 0.3348777 1,midg,midg; igrid,midg,midg -6.1199263E-02 0.5641862 gauss-seidel spectral radius is 0.9992775 estimated iterations to convergence 294 setup time was (sec) 2.250000 now iterating at: 04:31:53 rms-change max change #iterations 10.76434 528.9998 at 10iterations 6.316164 139.4736 at 20iterations 3.702351 83.11508 at 30iterations 2.163196 43.66260 at 40iterations 1.265575 25.92006 at 50iterations 0.7364388 12.67722 at 60iterations 0.4289177 8.455347 at 70iterations 0.2490601 4.506077 at 80iterations 0.1449860 2.570621 at 90iterations 8.4139451E-02 1.629240 at 100iterations 4.8806034E-02 0.8573456 at 110iterations 2.8402582E-02 0.4851227 at 120iterations 1.6507061E-02 0.2910128 at 130iterations 9.6043851E-03 0.1713562 at 140iterations 5.5961185E-03 9.7303391E-02 at 150iterations 3.2853147E-03 5.7880402E-02 at 160iterations 1.9405988E-03 3.7578583E-02 at 170iterations 1.1612485E-03 1.9845963E-02 at 180iterations finished qdiffx linear iterations at : 04:32:05 total time elapsed so far: 14.43000 # loops : 180 mean,max change (kT/e) : 1.1612485E-03 1.9845963E-02 energy calculations done at 14.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.67000 DelPhi exited at 04:32:06 14.674u 0.203s 0:15.63 95.1% 0+0k 0+0io 0pf+0w