Sun Oct 9 15:07:55 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 Sun Oct 9 2011 at 15:07:55 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5528 !!! WARNING: HIR 862 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5152849 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): -16.64500 52.44300 ymin,ymax (A): 98.36800 167.1420 zmin,zma (A): -34.98600 31.79000 x,y,z range (A): 69.08800 68.77402 66.77600 scale (grids/A): 0.5152849 object centre (A): 17.89900 132.7550 -1.598000 number of atom coordinates read : 5528 total number of charged atoms : 5354 net assigned charge : -3.985962 assigned positive charge : 849.7336 centred at (gu) : 89.68020 88.87355 89.07732 assigned negative charge : -853.7267 centred at (gu) : 89.67115 88.93712 89.06360 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 9053 nv = 96 ne = 84 npr = 112939 no. pairs analyzed = 112939 no. exposed pairs = 6494 no. arc points = 45524 no. surface atoms = 2188 nbur = 3340 mkacc time = 0.1900000 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 = 1.680000 m= 318 mr = 4918 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 22 time to turn everything in is 0.3500000 number of dielectric boundary points 4449 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4383 ## 635 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 12243 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.5731741E-10 -1.6394844E-11 midg,1,midg; midg,igrid,midg 2.2563509E-10 -2.3383351E-10 1,midg,midg; igrid,midg,midg -1.1517848E-10 -3.4912420E-11 gauss-seidel spectral radius is 0.9807808 estimated iterations to convergence 60 setup time was (sec) 0.5500000 now iterating at: 15:07:55 rms-change max change #iterations 7.8368478E-02 11.69650 at 10iterations 6.4671603E-03 0.9504051 at 20iterations 1.5188206E-03 0.2679520 at 30iterations 4.7791746E-04 8.2344055E-02 at 40iterations 1.5215551E-04 2.5997162E-02 at 50iterations finished qdiffx linear iterations at : 15:07:58 total time elapsed so far: 3.550000 # loops : 50 mean,max change (kT/e) : 1.5215551E-04 2.5997162E-02 energy calculations done at 3.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.680000 DelPhi exited at 15:07:59 3.687u 0.205s 0:04.26 91.0% 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 Sun Oct 9 2011 at 15:07:59 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5528 !!! WARNING: HIR 862 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.545855 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): -16.64500 52.44300 ymin,ymax (A): 98.36800 167.1420 zmin,zma (A): -34.98600 31.79000 x,y,z range (A): 69.08800 68.77402 66.77600 scale (grids/A): 1.545855 object centre (A): 17.89900 132.7550 -1.598000 number of atom coordinates read : 5528 total number of charged atoms : 5354 net assigned charge : -3.985962 assigned positive charge : 849.7336 centred at (gu) : 89.03884 86.61887 87.23026 assigned negative charge : -853.7267 centred at (gu) : 89.01340 86.81102 87.19051 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 103436 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45524 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 30704 mr = 72963 m= 2689 mr = 21111 m= 54 mr = 1228 m= 0 mr = 2 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 2376 time to turn everything in is 0.5100000 number of dielectric boundary points 41579 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 558 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 40311 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) : 0.5152849 object centre at (A) : 17.89900 132.7550 -1.598000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5616563E-02 -1.0462197E-02 midg,1,midg; midg,igrid,midg 2.5046634E-02 -1.7427426E-02 1,midg,midg; igrid,midg,midg -3.3708885E-02 -1.1881036E-02 gauss-seidel spectral radius is 0.9982003 estimated iterations to convergence 187 setup time was (sec) 0.7400000 now iterating at: 15:08:00 rms-change max change #iterations 4.283988 161.0118 at 10iterations 1.792749 56.75203 at 20iterations 0.7545155 22.94971 at 30iterations 0.3164777 9.487393 at 40iterations 0.1329740 4.056317 at 50iterations 5.6054905E-02 1.647293 at 60iterations 2.3727389E-02 0.6900692 at 70iterations 1.0254923E-02 0.3205471 at 80iterations 4.5571793E-03 0.1461220 at 90iterations 2.1495456E-03 7.6850891E-02 at 100iterations 1.1130742E-03 3.9497375E-02 at 110iterations 6.3192769E-04 2.3414612E-02 at 120iterations finished qdiffx linear iterations at : 15:08:07 total time elapsed so far: 8.210000 # loops : 120 mean,max change (kT/e) : 6.3192769E-04 2.3414612E-02 energy calculations done at 8.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.350000 DelPhi exited at 15:08:08 8.352u 0.212s 0:08.97 95.4% 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 Sun Oct 9 2011 at 15:08:08 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: 261 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5528 !!! WARNING: HIR 862 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.318782 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): -16.64500 52.44300 ymin,ymax (A): 98.36800 167.1420 zmin,zma (A): -34.98600 31.79000 x,y,z range (A): 69.08800 68.77402 66.77600 scale (grids/A): 2.318782 object centre (A): 17.89900 132.7550 -1.598000 number of atom coordinates read : 5528 total number of charged atoms : 5354 net assigned charge : -3.985962 assigned positive charge : 849.7336 centred at (gu) : 88.55786 84.92776 85.84489 assigned negative charge : -853.7267 centred at (gu) : 88.52007 85.21640 85.78584 start vw surface at 0.1500000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 241095 reading accessible surface arcs data from file ARCDAT no. of arc points read = 45524 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 109533 mr = 178964 m= 29061 mr = 87014 m= 3987 mr = 21587 m= 214 mr = 2464 m= 7 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 7732 time to turn everything in is 1.250000 number of dielectric boundary points 93810 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 69 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 42740 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) : 1.545855 object centre at (A) : 17.89900 132.7550 -1.598000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3190219 -0.2343161 midg,1,midg; midg,igrid,midg 0.5804139 -0.2745305 1,midg,midg; igrid,midg,midg -0.4040468 -0.3217813 gauss-seidel spectral radius is 0.9991945 estimated iterations to convergence 278 setup time was (sec) 1.510000 now iterating at: 15:08:10 rms-change max change #iterations 11.41158 267.5427 at 10iterations 6.569253 138.9747 at 20iterations 3.754950 93.19998 at 30iterations 2.130254 56.13968 at 40iterations 1.211931 27.66294 at 50iterations 0.6855569 15.30918 at 60iterations 0.3867115 7.955532 at 70iterations 0.2184174 3.957928 at 80iterations 0.1229749 2.186928 at 90iterations 6.9290884E-02 1.254147 at 100iterations 3.8933840E-02 0.7750969 at 110iterations 2.1937082E-02 0.3791885 at 120iterations 1.2339467E-02 0.2031326 at 130iterations 6.9660367E-03 0.1209393 at 140iterations 3.9353548E-03 7.3734283E-02 at 150iterations 2.2375775E-03 3.7837982E-02 at 160iterations 1.2825332E-03 2.1769404E-02 at 170iterations 7.4889231E-04 1.5256882E-02 at 180iterations finished qdiffx linear iterations at : 15:08:22 total time elapsed so far: 13.99000 # loops : 180 mean,max change (kT/e) : 7.4889231E-04 1.5256882E-02 energy calculations done at 13.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.13000 DelPhi exited at 15:08:23 14.130u 0.228s 0:14.69 97.6% 0+0k 0+0io 0pf+0w