Sun Oct 9 12:27:33 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 12:27:33 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2400 !!! WARNING: GLM 235 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: 0.6801421 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): -5.662000 43.96100 ymin,ymax (A): -14.08900 38.25300 zmin,zma (A): 2.067000 45.23900 x,y,z range (A): 49.62300 52.34200 43.17200 scale (grids/A): 0.6801421 object centre (A): 19.14950 12.08200 23.65300 number of atom coordinates read : 2400 total number of charged atoms : 2253 net assigned charge : 2.406025 assigned positive charge : 369.8880 centred at (gu) : 89.26587 90.72766 90.50603 assigned negative charge : -367.4823 centred at (gu) : 89.26804 90.93134 90.58156 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7375 nv = 96 ne = 84 npr = 48408 no. pairs analyzed = 48408 no. exposed pairs = 2967 no. arc points = 20665 no. surface atoms = 997 nbur = 1403 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 421 mr = 4083 m= 1 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 15 time to turn everything in is 0.1900000 number of dielectric boundary points 3647 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2024 ## 226 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8602 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0895521E-08 -1.3850916E-08 midg,1,midg; midg,igrid,midg 6.2641988E-08 -6.1918932E-08 1,midg,midg; igrid,midg,midg 1.3595130E-08 9.0398773E-09 gauss-seidel spectral radius is 0.9887704 estimated iterations to convergence 77 setup time was (sec) 0.3700000 now iterating at: 12:27:33 rms-change max change #iterations 0.1858981 31.34217 at 10iterations 2.1654956E-02 2.737831 at 20iterations 2.9413318E-03 0.4331970 at 30iterations 6.0974102E-04 9.5989227E-02 at 40iterations 1.7445484E-04 2.8013229E-02 at 50iterations finished qdiffx linear iterations at : 12:27:36 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 1.7445484E-04 2.8013229E-02 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 12:27:37 3.327u 0.168s 0:03.77 92.3% 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 12:27:37 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2400 !!! WARNING: GLM 235 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: 2.040426 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): -5.662000 43.96100 ymin,ymax (A): -14.08900 38.25300 zmin,zma (A): 2.067000 45.23900 x,y,z range (A): 49.62300 52.34200 43.17200 scale (grids/A): 2.040426 object centre (A): 19.14950 12.08200 23.65300 number of atom coordinates read : 2400 total number of charged atoms : 2253 net assigned charge : 2.406025 assigned positive charge : 369.8880 centred at (gu) : 87.79689 92.18224 91.51772 assigned negative charge : -367.4823 centred at (gu) : 87.80365 92.79369 91.74441 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 79392 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20665 grid for indexing accessible points = 1.400000 m= 29328 mr = 55607 m= 4913 mr = 21509 m= 419 mr = 3146 m= 9 mr = 229 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 254 time to turn everything in is 0.3800000 number of dielectric boundary points 33570 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 148 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 17847 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) : 0.6801421 object centre at (A) : 19.14950 12.08200 23.65300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8778374E-02 6.5547423E-03 midg,1,midg; midg,igrid,midg 2.0787906E-02 -8.8381514E-02 1,midg,midg; igrid,midg,midg 3.3500258E-02 -1.1069220E-02 gauss-seidel spectral radius is 0.9987829 estimated iterations to convergence 227 setup time was (sec) 0.6000000 now iterating at: 12:27:37 rms-change max change #iterations 4.742927 193.6058 at 10iterations 2.308203 78.06020 at 20iterations 1.124043 36.96883 at 30iterations 0.5504915 16.27469 at 40iterations 0.2686565 8.867876 at 50iterations 0.1312040 3.902031 at 60iterations 6.4527795E-02 1.935720 at 70iterations 3.1641833E-02 0.9095192 at 80iterations 1.5592286E-02 0.4291153 at 90iterations 7.7677672E-03 0.2677689 at 100iterations 3.9138398E-03 0.1306686 at 110iterations 2.0409094E-03 5.9055328E-02 at 120iterations finished qdiffx linear iterations at : 12:27:44 total time elapsed so far: 7.610000 # loops : 120 mean,max change (kT/e) : 2.0409094E-03 5.9055328E-02 energy calculations done at 7.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.740000 DelPhi exited at 12:27:45 7.747u 0.185s 0:08.20 96.5% 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 Sun Oct 9 2011 at 12:27:45 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: 322 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2400 !!! WARNING: GLM 235 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: 3.060639 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): -5.662000 43.96100 ymin,ymax (A): -14.08900 38.25300 zmin,zma (A): 2.067000 45.23900 x,y,z range (A): 49.62300 52.34200 43.17200 scale (grids/A): 3.060639 object centre (A): 19.14950 12.08200 23.65300 number of atom coordinates read : 2400 total number of charged atoms : 2253 net assigned charge : 2.406025 assigned positive charge : 369.8880 centred at (gu) : 86.69520 93.27338 92.27647 assigned negative charge : -367.4823 centred at (gu) : 86.70541 94.19047 92.61658 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 182956 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20665 grid for indexing accessible points = 1.400000 m= 94697 mr = 134033 m= 34819 mr = 77626 m= 9001 mr = 27930 m= 1701 mr = 6786 m= 189 mr = 1247 m= 1 mr = 109 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 923 time to turn everything in is 1.020000 number of dielectric boundary points 75633 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 18024 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) : 2.040426 object centre at (A) : 19.14950 12.08200 23.65300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4530579 -9.1436245E-03 midg,1,midg; midg,igrid,midg 0.4895500 -1.002476 1,midg,midg; igrid,midg,midg 0.3110823 -0.2952917 gauss-seidel spectral radius is 0.9992873 estimated iterations to convergence 296 setup time was (sec) 1.240000 now iterating at: 12:27:46 rms-change max change #iterations 10.82306 434.3761 at 10iterations 6.388729 140.6694 at 20iterations 3.773180 74.42702 at 30iterations 2.215968 49.48202 at 40iterations 1.300323 26.07201 at 50iterations 0.7604088 16.23551 at 60iterations 0.4452149 8.069782 at 70iterations 0.2611412 5.156052 at 80iterations 0.1524156 2.906984 at 90iterations 8.8954896E-02 1.651589 at 100iterations 5.2100219E-02 0.8726654 at 110iterations 3.0599635E-02 0.5398407 at 120iterations 1.8098677E-02 0.2974968 at 130iterations 1.0893686E-02 0.2022171 at 140iterations 6.7078546E-03 0.1355133 at 150iterations 4.2831036E-03 8.8489532E-02 at 160iterations 2.8929834E-03 6.7344666E-02 at 170iterations 2.0701722E-03 4.5234680E-02 at 180iterations finished qdiffx linear iterations at : 12:27:58 total time elapsed so far: 12.56000 # loops : 180 mean,max change (kT/e) : 2.0701722E-03 4.5234680E-02 energy calculations done at 12.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.69000 DelPhi exited at 12:27:58 12.690u 0.219s 0:13.18 97.8% 0+0k 0+0io 0pf+0w