Tue Oct 11 08:10:00 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 08:10:00 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: 241 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2325 !!! WARNING: WAT 2 has a net charge of -0.8340 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5775002 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): -22.03700 28.46600 ymin,ymax (A): 21.88400 83.52900 zmin,zma (A): 2.340000 51.99300 x,y,z range (A): 50.50300 61.64500 49.65300 scale (grids/A): 0.5775002 object centre (A): 3.214500 52.70650 27.16650 number of atom coordinates read : 2325 total number of charged atoms : 2185 net assigned charge : 3.666011 assigned positive charge : 347.4163 centred at (gu) : 90.00473 86.80416 91.95396 assigned negative charge : -343.7509 centred at (gu) : 89.84730 86.75805 91.84792 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5206 nv = 96 ne = 84 npr = 46368 no. pairs analyzed = 46368 no. exposed pairs = 3088 no. arc points = 22042 no. surface atoms = 1027 nbur = 1298 mkacc time = 0.1000000 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 = 1.484000 m= 226 mr = 2617 m= 3 mr = 16 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.2900000 number of dielectric boundary points 2802 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2240 ## 265 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 6510 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.8078903E-10 3.7052177E-09 midg,1,midg; midg,igrid,midg -5.9097796E-11 6.8348455E-10 1,midg,midg; igrid,midg,midg -1.7526756E-09 3.0954932E-09 gauss-seidel spectral radius is 0.9844760 estimated iterations to convergence 66 setup time was (sec) 0.5000000 now iterating at: 08:10:01 rms-change max change #iterations 8.4176347E-02 14.77354 at 10iterations 6.5317061E-03 1.135334 at 20iterations 6.2630011E-04 0.1164742 at 30iterations 1.1810342E-04 3.1919479E-02 at 40iterations 3.3214004E-05 9.3917847E-03 at 50iterations finished qdiffx linear iterations at : 08:10:03 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 3.3214004E-05 9.3917847E-03 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 08:10:04 3.114u 0.156s 0:03.90 83.5% 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 08:10:04 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: 241 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2325 !!! WARNING: WAT 2 has a net charge of -0.8340 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.732501 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): -22.03700 28.46600 ymin,ymax (A): 21.88400 83.52900 zmin,zma (A): 2.340000 51.99300 x,y,z range (A): 50.50300 61.64500 49.65300 scale (grids/A): 1.732501 object centre (A): 3.214500 52.70650 27.16650 number of atom coordinates read : 2325 total number of charged atoms : 2185 net assigned charge : 3.666011 assigned positive charge : 347.4163 centred at (gu) : 90.01385 80.41207 95.86160 assigned negative charge : -343.7509 centred at (gu) : 89.54185 80.27409 95.54356 start vw surface at 0.1300000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 56728 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22042 grid for indexing accessible points = 1.400000 m= 17582 mr = 37418 m= 2049 mr = 11942 m= 73 mr = 1051 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 351 time to turn everything in is 0.4000000 number of dielectric boundary points 26001 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 218 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 16892 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) : 0.5775002 object centre at (A) : 3.214500 52.70650 27.16650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1414009E-03 1.3291330E-02 midg,1,midg; midg,igrid,midg 2.4745714E-02 2.5030958E-02 1,midg,midg; igrid,midg,midg -8.5876929E-03 1.4438119E-02 gauss-seidel spectral radius is 0.9983189 estimated iterations to convergence 194 setup time was (sec) 0.6600000 now iterating at: 08:10:05 rms-change max change #iterations 3.278232 173.0060 at 10iterations 1.401465 64.57626 at 20iterations 0.6015108 22.81608 at 30iterations 0.2591648 9.724863 at 40iterations 0.1112889 4.184148 at 50iterations 4.7971837E-02 1.715952 at 60iterations 2.0701550E-02 0.8210497 at 70iterations 8.9381728E-03 0.3563957 at 80iterations 3.8670711E-03 0.1478672 at 90iterations 1.7155297E-03 7.7577591E-02 at 100iterations 7.8422012E-04 3.1940460E-02 at 110iterations 3.8506297E-04 1.8518448E-02 at 120iterations finished qdiffx linear iterations at : 08:10:11 total time elapsed so far: 6.760000 # loops : 120 mean,max change (kT/e) : 3.8506297E-04 1.8518448E-02 energy calculations done at 6.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.950000 DelPhi exited at 08:10:12 6.950u 0.192s 0:07.61 93.8% 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 08:10:12 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: 241 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2325 !!! WARNING: WAT 2 has a net charge of -0.8340 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.598751 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): -22.03700 28.46600 ymin,ymax (A): 21.88400 83.52900 zmin,zma (A): 2.340000 51.99300 x,y,z range (A): 50.50300 61.64500 49.65300 scale (grids/A): 2.598751 object centre (A): 3.214500 52.70650 27.16650 number of atom coordinates read : 2325 total number of charged atoms : 2185 net assigned charge : 3.666011 assigned positive charge : 347.4163 centred at (gu) : 90.02071 75.61810 98.79243 assigned negative charge : -343.7509 centred at (gu) : 89.31274 75.41110 98.31539 start vw surface at 0.1400000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 131556 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22042 grid for indexing accessible points = 1.400000 m= 60364 mr = 91713 m= 17821 mr = 47433 m= 3272 mr = 13202 m= 299 mr = 2189 m= 14 mr = 182 m= 0 mr = 0 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 1237 time to turn everything in is 1.000000 number of dielectric boundary points 58607 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 6 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 17471 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) : 1.732501 object centre at (A) : 3.214500 52.70650 27.16650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.4904177E-02 0.1313823 midg,1,midg; midg,igrid,midg 0.3278569 0.3594295 1,midg,midg; igrid,midg,midg -8.1536755E-02 0.1963178 gauss-seidel spectral radius is 0.9991652 estimated iterations to convergence 273 setup time was (sec) 1.280000 now iterating at: 08:10:13 rms-change max change #iterations 8.310226 273.6563 at 10iterations 4.722988 130.1169 at 20iterations 2.672632 68.67598 at 30iterations 1.503185 38.55280 at 40iterations 0.8430960 22.34647 at 50iterations 0.4714121 11.41701 at 60iterations 0.2638034 5.976732 at 70iterations 0.1467479 3.280384 at 80iterations 8.1672624E-02 1.758612 at 90iterations 4.5491256E-02 1.012143 at 100iterations 2.5286948E-02 0.6644201 at 110iterations 1.4070576E-02 0.3520327 at 120iterations 7.8547578E-03 0.1724222 at 130iterations 4.3957913E-03 0.1052344 at 140iterations 2.4701308E-03 5.7765961E-02 at 150iterations 1.4136815E-03 4.0412903E-02 at 160iterations 8.2763203E-04 2.2869110E-02 at 170iterations 5.0828746E-04 1.4823914E-02 at 180iterations finished qdiffx linear iterations at : 08:10:23 total time elapsed so far: 11.06000 # loops : 180 mean,max change (kT/e) : 5.0828746E-04 1.4823914E-02 energy calculations done at 11.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.24000 DelPhi exited at 08:10:23 11.239u 0.190s 0:11.77 97.0% 0+0k 0+0io 0pf+0w