Sun Oct 9 02:29:13 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 Sun Oct 9 2011 at 02:29:13 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2013 !!! WARNING: MG2 214 has a net charge of 1.4000 !!! WARNING: SAM 215 has a net charge of -0.6000 !!! WARNING: SAM 1 has a net charge of -0.5000 !!! WARNING: SAM 4 has a net charge of 0.4200 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: 0.7079083 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): -45.18300 5.106000 ymin,ymax (A): 49.93400 88.09700 zmin,zma (A): 23.30300 66.78500 x,y,z range (A): 50.28900 38.16300 43.48200 scale (grids/A): 0.7079083 object centre (A): -20.03850 69.01550 45.04400 number of atom coordinates read : 2013 total number of charged atoms : 1932 net assigned charge : -3.279994 assigned positive charge : 306.0268 centred at (gu) : 90.14308 89.29661 89.25681 assigned negative charge : -309.3072 centred at (gu) : 90.20802 89.32195 89.27838 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7099 nv = 96 ne = 84 npr = 40404 no. pairs analyzed = 40404 no. exposed pairs = 2261 no. arc points = 15839 no. surface atoms = 771 nbur = 1242 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 491 mr = 4368 m= 3 mr = 149 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 294 time to turn everything in is 0.3000000 number of dielectric boundary points 3076 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1434 ## 117 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7804 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9939165E-08 -3.3675853E-08 midg,1,midg; midg,igrid,midg -1.7661399E-08 -3.5558429E-08 1,midg,midg; igrid,midg,midg 3.7007770E-09 -6.2146484E-08 gauss-seidel spectral radius is 0.9895941 estimated iterations to convergence 80 setup time was (sec) 0.5700000 now iterating at: 02:29:14 rms-change max change #iterations 0.2042045 29.60544 at 10iterations 2.4654977E-02 3.183022 at 20iterations 3.0748323E-03 0.4379044 at 30iterations 3.7724708E-04 5.3312302E-02 at 40iterations 4.7233461E-05 6.7977905E-03 at 50iterations finished qdiffx linear iterations at : 02:29:17 total time elapsed so far: 3.980000 # loops : 50 mean,max change (kT/e) : 4.7233461E-05 6.7977905E-03 energy calculations done at 3.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.170000 DelPhi exited at 02:29:18 4.173u 0.289s 0:04.80 92.7% 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 Sun Oct 9 2011 at 02:29:18 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2013 !!! WARNING: MG2 214 has a net charge of 1.4000 !!! WARNING: SAM 215 has a net charge of -0.6000 !!! WARNING: SAM 1 has a net charge of -0.5000 !!! WARNING: SAM 4 has a net charge of 0.4200 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: 2.123725 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): -45.18300 5.106000 ymin,ymax (A): 49.93400 88.09700 zmin,zma (A): 23.30300 66.78500 x,y,z range (A): 50.28900 38.16300 43.48200 scale (grids/A): 2.123725 object centre (A): -20.03850 69.01550 45.04400 number of atom coordinates read : 2013 total number of charged atoms : 1932 net assigned charge : -3.279994 assigned positive charge : 306.0268 centred at (gu) : 90.42908 87.88947 87.77020 assigned negative charge : -309.3072 centred at (gu) : 90.62399 87.96584 87.83521 start vw surface at 0.1200000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 75736 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15839 grid for indexing accessible points = 1.400000 m= 32481 mr = 55606 m= 7303 mr = 26118 m= 747 mr = 5661 m= 15 mr = 484 m= 0 mr = 1 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 7388 time to turn everything in is 0.6600000 number of dielectric boundary points 28412 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 60 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 15376 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) : 0.7079083 object centre at (A) : -20.03850 69.01550 45.04400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8944628E-02 2.9158443E-03 midg,1,midg; midg,igrid,midg -2.2802461E-02 -1.2767558E-02 1,midg,midg; igrid,midg,midg -1.2865156E-02 1.1687929E-02 gauss-seidel spectral radius is 0.9988232 estimated iterations to convergence 231 setup time was (sec) 0.9500000 now iterating at: 02:29:19 rms-change max change #iterations 4.577798 173.3685 at 10iterations 2.254832 77.43841 at 20iterations 1.118192 33.55389 at 30iterations 0.5547739 17.92623 at 40iterations 0.2746603 8.918018 at 50iterations 0.1360178 4.852455 at 60iterations 6.7437135E-02 2.028535 at 70iterations 3.3344101E-02 1.019676 at 80iterations 1.6490931E-02 0.4754219 at 90iterations 8.1810327E-03 0.2566833 at 100iterations 4.0441705E-03 0.1346956 at 110iterations 2.0075184E-03 6.6234589E-02 at 120iterations finished qdiffx linear iterations at : 02:29:28 total time elapsed so far: 9.570000 # loops : 120 mean,max change (kT/e) : 2.0075184E-03 6.6234589E-02 energy calculations done at 9.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.760000 DelPhi exited at 02:29:28 9.758u 0.365s 0:10.40 97.2% 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 Sun Oct 9 2011 at 02:29:28 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2013 !!! WARNING: MG2 214 has a net charge of 1.4000 !!! WARNING: SAM 215 has a net charge of -0.6000 !!! WARNING: SAM 1 has a net charge of -0.5000 !!! WARNING: SAM 4 has a net charge of 0.4200 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: 3.185587 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): -45.18300 5.106000 ymin,ymax (A): 49.93400 88.09700 zmin,zma (A): 23.30300 66.78500 x,y,z range (A): 50.28900 38.16300 43.48200 scale (grids/A): 3.185587 object centre (A): -20.03850 69.01550 45.04400 number of atom coordinates read : 2013 total number of charged atoms : 1932 net assigned charge : -3.279994 assigned positive charge : 306.0268 centred at (gu) : 90.64360 86.83418 86.65530 assigned negative charge : -309.3072 centred at (gu) : 90.93601 86.94887 86.75275 start vw surface at 0.1600000 fill in re-entrant regions at 0.9800000 boundary points on vw surface= 174498 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15839 grid for indexing accessible points = 1.400000 m= 98942 mr = 132931 m= 44141 mr = 85064 m= 14410 mr = 38304 m= 3249 mr = 12426 m= 403 mr = 2679 m= 20 mr = 271 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 1.110000 no. cavity mid-points inaccessible to solvent = 25405 time to turn everything in is 2.200000 number of dielectric boundary points 63985 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.350000 number of grid points assigned charge 15456 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) : 2.123725 object centre at (A) : -20.03850 69.01550 45.04400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3230849 0.1603318 midg,1,midg; midg,igrid,midg -0.1727400 -0.1037203 1,midg,midg; igrid,midg,midg -0.2079423 0.1276522 gauss-seidel spectral radius is 0.9992855 estimated iterations to convergence 295 setup time was (sec) 2.540000 now iterating at: 02:29:31 rms-change max change #iterations 10.04808 315.0278 at 10iterations 5.829432 110.9000 at 20iterations 3.381377 62.01306 at 30iterations 1.960620 35.71756 at 40iterations 1.137657 20.37396 at 50iterations 0.6614472 11.98621 at 60iterations 0.3827517 6.237457 at 70iterations 0.2221986 4.020440 at 80iterations 0.1285229 2.426726 at 90iterations 7.4639827E-02 1.402649 at 100iterations 4.3223016E-02 0.7104616 at 110iterations 2.5023736E-02 0.4509850 at 120iterations 1.4550472E-02 0.2464275 at 130iterations 8.4163602E-03 0.1526012 at 140iterations 4.8849047E-03 8.1533909E-02 at 150iterations 2.8334183E-03 4.7068596E-02 at 160iterations 1.6454225E-03 2.8530121E-02 at 170iterations 9.5183501E-04 1.7317057E-02 at 180iterations finished qdiffx linear iterations at : 02:29:45 total time elapsed so far: 16.65000 # loops : 180 mean,max change (kT/e) : 9.5183501E-04 1.7317057E-02 energy calculations done at 16.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.84000 DelPhi exited at 02:29:46 16.842u 0.313s 0:17.43 98.3% 0+0k 0+0io 0pf+0w