Tue Oct 11 06:02:55 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 Tue Oct 11 2011 at 06:02:55 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2339 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 0.7081195 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): 25.79900 72.25500 ymin,ymax (A): -18.77300 31.50100 zmin,zma (A): 3.996000 46.31400 x,y,z range (A): 46.45600 50.27400 42.31800 scale (grids/A): 0.7081195 object centre (A): 49.02700 6.364000 25.15500 number of atom coordinates read : 2339 total number of charged atoms : 2007 net assigned charge : 5.945011 assigned positive charge : 328.9029 centred at (gu) : 89.28106 90.29373 90.32431 assigned negative charge : -322.9580 centred at (gu) : 89.41280 90.23245 90.40214 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7203 nv = 96 ne = 84 npr = 42934 no. pairs analyzed = 42934 no. exposed pairs = 2580 no. arc points = 17637 no. surface atoms = 881 nbur = 1458 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 471 mr = 4161 m= 3 mr = 92 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3424 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1620 ## 150 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8019 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.5160714E-08 1.0201219E-08 midg,1,midg; midg,igrid,midg 1.7596721E-08 8.6947864E-08 1,midg,midg; igrid,midg,midg 1.3587722E-07 -1.5953859E-08 gauss-seidel spectral radius is 0.9896069 estimated iterations to convergence 80 setup time was (sec) 0.3900000 now iterating at: 06:02:56 rms-change max change #iterations 0.2063132 34.46462 at 10iterations 2.6236299E-02 3.250206 at 20iterations 3.4673412E-03 0.4800911 at 30iterations 5.9487420E-04 9.2597961E-02 at 40iterations 1.5409020E-04 1.9996643E-02 at 50iterations finished qdiffx linear iterations at : 06:02:59 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 1.5409020E-04 1.9996643E-02 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 06:03:00 3.550u 0.228s 0:04.61 81.7% 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 06:03:00 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2339 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 2.124359 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): 25.79900 72.25500 ymin,ymax (A): -18.77300 31.50100 zmin,zma (A): 3.996000 46.31400 x,y,z range (A): 46.45600 50.27400 42.31800 scale (grids/A): 2.124359 object centre (A): 49.02700 6.364000 25.15500 number of atom coordinates read : 2339 total number of charged atoms : 2007 net assigned charge : 5.945011 assigned positive charge : 328.9029 centred at (gu) : 87.84333 90.88106 90.97275 assigned negative charge : -322.9580 centred at (gu) : 88.23828 90.69739 91.20649 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 76523 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17637 grid for indexing accessible points = 1.400000 m= 31071 mr = 54689 m= 6021 mr = 23738 m= 561 mr = 4087 m= 13 mr = 288 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 31387 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 67 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 15916 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) : 0.7081195 object centre at (A) : 49.02700 6.364000 25.15500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0150080E-02 2.8063744E-02 midg,1,midg; midg,igrid,midg 3.8304318E-02 2.7051881E-02 1,midg,midg; igrid,midg,midg 4.5613814E-02 -4.8761532E-02 gauss-seidel spectral radius is 0.9988353 estimated iterations to convergence 232 setup time was (sec) 0.6500000 now iterating at: 06:03:01 rms-change max change #iterations 4.735226 244.0348 at 10iterations 2.339480 86.96281 at 20iterations 1.165152 36.41730 at 30iterations 0.5789800 16.55327 at 40iterations 0.2886288 8.083479 at 50iterations 0.1432300 4.177421 at 60iterations 7.1209460E-02 1.971434 at 70iterations 3.5480391E-02 1.046545 at 80iterations 1.7717319E-02 0.5683994 at 90iterations 8.9170597E-03 0.2755051 at 100iterations 4.4972850E-03 0.1321831 at 110iterations 2.3258210E-03 7.4764252E-02 at 120iterations finished qdiffx linear iterations at : 06:03:08 total time elapsed so far: 8.130000 # loops : 120 mean,max change (kT/e) : 2.3258210E-03 7.4764252E-02 energy calculations done at 8.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.270000 DelPhi exited at 06:03:09 8.273u 0.234s 0:08.86 95.9% 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 06:03:09 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: 323 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2339 !!! WARNING: HIQ 57 has a net charge of 0.5140 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 has a net charge of -0.0940 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: 3.186538 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): 25.79900 72.25500 ymin,ymax (A): -18.77300 31.50100 zmin,zma (A): 3.996000 46.31400 x,y,z range (A): 46.45600 50.27400 42.31800 scale (grids/A): 3.186538 object centre (A): 49.02700 6.364000 25.15500 number of atom coordinates read : 2339 total number of charged atoms : 2007 net assigned charge : 5.945011 assigned positive charge : 328.9029 centred at (gu) : 86.76482 91.32162 91.45913 assigned negative charge : -322.9580 centred at (gu) : 87.35741 91.04610 91.80962 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 176279 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17637 grid for indexing accessible points = 1.400000 m= 96654 mr = 131475 m= 39425 mr = 80806 m= 11444 mr = 32567 m= 2305 mr = 8995 m= 271 mr = 1715 m= 15 mr = 180 m= 0 mr = 0 time to grow re-entrant surface = 0.6300001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.220000 number of dielectric boundary points 70655 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 16056 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) : 2.124359 object centre at (A) : 49.02700 6.364000 25.15500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1062952 0.2443133 midg,1,midg; midg,igrid,midg 0.2945158 0.1428663 1,midg,midg; igrid,midg,midg 0.4399191 -0.5995124 gauss-seidel spectral radius is 0.9992970 estimated iterations to convergence 298 setup time was (sec) 1.460000 now iterating at: 06:03:11 rms-change max change #iterations 10.49374 390.6451 at 10iterations 6.208641 133.6527 at 20iterations 3.668828 80.13702 at 30iterations 2.162461 44.24152 at 40iterations 1.272271 23.28506 at 50iterations 0.7479518 13.82215 at 60iterations 0.4386138 7.985835 at 70iterations 0.2584615 4.840020 at 80iterations 0.1514569 2.993180 at 90iterations 8.8872641E-02 1.670391 at 100iterations 5.2240729E-02 0.9508228 at 110iterations 3.0810447E-02 0.5526791 at 120iterations 1.8345604E-02 0.3179970 at 130iterations 1.1069610E-02 0.1981964 at 140iterations 6.8705701E-03 0.1264572 at 150iterations 4.4152038E-03 8.7196350E-02 at 160iterations 2.9870349E-03 5.2986145E-02 at 170iterations 2.1432205E-03 3.7483215E-02 at 180iterations finished qdiffx linear iterations at : 06:03:22 total time elapsed so far: 13.11000 # loops : 180 mean,max change (kT/e) : 2.1432205E-03 3.7483215E-02 energy calculations done at 13.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.25000 DelPhi exited at 06:03:23 13.249u 0.255s 0:14.28 94.4% 0+0k 0+0io 0pf+0w