Tue Oct 11 07:49:25 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 Tue Oct 11 2011 at 07:49:25 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2770 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6351132 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): -13.29500 42.75800 ymin,ymax (A): -21.69300 26.60900 zmin,zma (A): -11.65600 40.30400 x,y,z range (A): 56.05300 48.30200 51.96000 scale (grids/A): 0.6351132 object centre (A): 14.73150 2.457999 14.32400 number of atom coordinates read : 2770 total number of charged atoms : 2406 net assigned charge : 9.500012 assigned positive charge : 386.6590 centred at (gu) : 90.04363 88.31811 90.85423 assigned negative charge : -377.1597 centred at (gu) : 90.05753 88.28440 91.04681 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6695 nv = 96 ne = 84 npr = 51872 no. pairs analyzed = 51872 no. exposed pairs = 2956 no. arc points = 20400 no. surface atoms = 1008 nbur = 1762 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 333 mr = 3824 m= 0 mr = 46 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3158 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2081 ## 237 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8099 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5692108E-08 -8.8341414E-09 midg,1,midg; midg,igrid,midg 1.2567297E-08 1.0945471E-08 1,midg,midg; igrid,midg,midg 1.3476166E-08 1.0953969E-08 gauss-seidel spectral radius is 0.9871443 estimated iterations to convergence 72 setup time was (sec) 0.3700000 now iterating at: 07:49:25 rms-change max change #iterations 0.1398077 20.81355 at 10iterations 1.3813633E-02 1.856563 at 20iterations 1.5489659E-03 0.2222328 at 30iterations 2.3203269E-04 3.3473969E-02 at 40iterations 4.7007834E-05 7.3127747E-03 at 50iterations finished qdiffx linear iterations at : 07:49:28 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 4.7007834E-05 7.3127747E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 07:49:29 3.322u 0.184s 0:03.82 91.6% 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 07:49:29 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2770 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.905340 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): -13.29500 42.75800 ymin,ymax (A): -21.69300 26.60900 zmin,zma (A): -11.65600 40.30400 x,y,z range (A): 56.05300 48.30200 51.96000 scale (grids/A): 1.905340 object centre (A): 14.73150 2.457999 14.32400 number of atom coordinates read : 2770 total number of charged atoms : 2406 net assigned charge : 9.500012 assigned positive charge : 386.6590 centred at (gu) : 90.13015 84.95393 92.56226 assigned negative charge : -377.1597 centred at (gu) : 90.17254 84.85319 93.14023 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 72654 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20400 grid for indexing accessible points = 1.400000 m= 26617 mr = 51515 m= 4011 mr = 20159 m= 252 mr = 2457 m= 4 mr = 98 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 649 time to turn everything in is 0.3600000 number of dielectric boundary points 29309 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 168 iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 18861 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) : 0.6351132 object centre at (A) : 14.73150 2.457999 14.32400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3409323E-02 -8.2589593E-03 midg,1,midg; midg,igrid,midg 1.3685054E-02 2.3623459E-02 1,midg,midg; igrid,midg,midg 2.1474916E-02 3.0514095E-02 gauss-seidel spectral radius is 0.9986203 estimated iterations to convergence 213 setup time was (sec) 0.5700000 now iterating at: 07:49:29 rms-change max change #iterations 4.143999 168.1011 at 10iterations 1.943982 71.17471 at 20iterations 0.9064993 31.09713 at 30iterations 0.4232320 13.45154 at 40iterations 0.1983566 7.372840 at 50iterations 9.2834130E-02 2.897225 at 60iterations 4.3372739E-02 1.293856 at 70iterations 2.0315645E-02 0.6463024 at 80iterations 9.5727369E-03 0.2979012 at 90iterations 4.5264279E-03 0.1496983 at 100iterations 2.1521528E-03 7.1877480E-02 at 110iterations 1.0447914E-03 3.3487320E-02 at 120iterations finished qdiffx linear iterations at : 07:49:36 total time elapsed so far: 7.510000 # loops : 120 mean,max change (kT/e) : 1.0447914E-03 3.3487320E-02 energy calculations done at 7.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 07:49:37 7.648u 0.186s 0:08.36 93.5% 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 07:49:37 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2770 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.858009 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): -13.29500 42.75800 ymin,ymax (A): -21.69300 26.60900 zmin,zma (A): -11.65600 40.30400 x,y,z range (A): 56.05300 48.30200 51.96000 scale (grids/A): 2.858009 object centre (A): 14.73150 2.457999 14.32400 number of atom coordinates read : 2770 total number of charged atoms : 2406 net assigned charge : 9.500012 assigned positive charge : 386.6590 centred at (gu) : 90.19523 82.43076 93.84304 assigned negative charge : -377.1597 centred at (gu) : 90.25883 82.27978 94.71017 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 167901 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20400 grid for indexing accessible points = 1.400000 m= 86813 mr = 124344 m= 30925 mr = 72252 m= 7004 mr = 25060 m= 1048 mr = 5247 m= 75 mr = 731 m= 3 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 2359 time to turn everything in is 0.9400000 number of dielectric boundary points 66103 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 19245 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) : 1.905340 object centre at (A) : 14.73150 2.457999 14.32400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6968365 -0.1811718 midg,1,midg; midg,igrid,midg 0.1087337 0.2740717 1,midg,midg; igrid,midg,midg 0.1314555 0.1606373 gauss-seidel spectral radius is 0.9992428 estimated iterations to convergence 287 setup time was (sec) 1.180000 now iterating at: 07:49:38 rms-change max change #iterations 9.629627 365.7052 at 10iterations 5.554327 123.8582 at 20iterations 3.186746 60.00778 at 30iterations 1.831131 38.47691 at 40iterations 1.047391 20.04221 at 50iterations 0.6000822 11.18439 at 60iterations 0.3430622 6.388027 at 70iterations 0.1959399 3.538802 at 80iterations 0.1121023 2.014860 at 90iterations 6.3981615E-02 1.296957 at 100iterations 3.6596186E-02 0.6505966 at 110iterations 2.0977147E-02 0.3762131 at 120iterations 1.2030764E-02 0.2192574 at 130iterations 6.9171372E-03 0.1311226 at 140iterations 4.0097805E-03 7.4260712E-02 at 150iterations 2.3573099E-03 4.3868065E-02 at 160iterations 1.4045198E-03 2.8266907E-02 at 170iterations 8.6483528E-04 1.8062592E-02 at 180iterations finished qdiffx linear iterations at : 07:49:50 total time elapsed so far: 12.27000 # loops : 180 mean,max change (kT/e) : 8.6483528E-04 1.8062592E-02 energy calculations done at 12.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.40000 DelPhi exited at 07:49:50 12.399u 0.189s 0:12.97 96.9% 0+0k 0+0io 0pf+0w