Wed Feb 15 08:56:54 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:56:55 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5868 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 grid size : 179 scale,in grids/A, set to be: 0.4820060 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): -55.32700 18.53100 ymin,ymax (A): -35.61000 28.11900 zmin,zma (A): 28.96800 94.33000 x,y,z range (A): 73.85800 63.72900 65.36200 scale (grids/A): 0.4820060 object centre (A): -18.39800 -3.745501 61.64900 number of atom coordinates read : 5868 total number of charged atoms : 5698 net assigned charge : -4.999963 assigned positive charge : 879.0463 centred at (gu) : 90.21267 89.73979 89.16846 assigned negative charge : -884.0535 centred at (gu) : 90.33367 89.72366 89.13573 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 8469 nv = 96 ne = 84 npr = 118242 no. pairs analyzed = 118242 no. exposed pairs = 7424 no. arc points = 51768 no. surface atoms = 2487 nbur = 3381 mkacc time = 0.2800000 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 = 1.764000 m= 284 mr = 4273 m= 0 mr = 1 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 4479 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4880 ## 844 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 11635 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.8902348E-11 8.4781409E-12 midg,1,midg; midg,igrid,midg -3.4374191E-11 -3.4197018E-12 1,midg,midg; igrid,midg,midg 8.1762770E-11 -1.3380529E-10 gauss-seidel spectral radius is 0.9780807 estimated iterations to convergence 56 setup time was (sec) 0.7900000 now iterating at: 08:56:56 rms-change max change #iterations 5.4647237E-02 7.629013 at 10iterations 3.0932021E-03 0.6423721 at 20iterations 4.4822291E-04 0.1151657 at 30iterations 1.2053404E-04 2.9327393E-02 at 40iterations 3.5539102E-05 7.9078674E-03 at 50iterations finished qdiffx linear iterations at : 08:56:58 total time elapsed so far: 3.490000 # loops : 50 mean,max change (kT/e) : 3.5539102E-05 7.9078674E-03 energy calculations done at 3.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.680000 DelPhi exited at 08:56:59 3.683u 0.201s 0:04.22 91.9% 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 Wed Feb 15 2012 at 08:56:59 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5868 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 grid size : 179 scale,in grids/A, set to be: 1.446018 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): -55.32700 18.53100 ymin,ymax (A): -35.61000 28.11900 zmin,zma (A): 28.96800 94.33000 x,y,z range (A): 73.85800 63.72900 65.36200 scale (grids/A): 1.446018 object centre (A): -18.39800 -3.745501 61.64900 number of atom coordinates read : 5868 total number of charged atoms : 5698 net assigned charge : -4.999963 assigned positive charge : 879.0463 centred at (gu) : 90.63618 89.21745 87.50360 assigned negative charge : -884.0535 centred at (gu) : 91.00068 89.17065 87.40661 start vw surface at 0.2300000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 97110 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51768 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 26312 mr = 65901 m= 1817 mr = 16887 m= 24 mr = 650 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 967 time to turn everything in is 0.7500000 number of dielectric boundary points 41825 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 829 ## 24 charges are in solution ## iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 41895 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) : 0.4820060 object centre at (A) : -18.39800 -3.745501 61.64900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1205778E-02 -3.7771973E-03 midg,1,midg; midg,igrid,midg 8.2265568E-04 1.7406337E-03 1,midg,midg; igrid,midg,midg 5.5456758E-03 -1.1539145E-02 gauss-seidel spectral radius is 0.9979583 estimated iterations to convergence 176 setup time was (sec) 1.060000 now iterating at: 08:57:00 rms-change max change #iterations 3.735884 144.1329 at 10iterations 1.478015 52.79606 at 20iterations 0.5855926 18.88686 at 30iterations 0.2327738 7.621185 at 40iterations 9.2193492E-02 2.918005 at 50iterations 3.6785662E-02 1.136144 at 60iterations 1.4654648E-02 0.5323038 at 70iterations 5.8753947E-03 0.1843834 at 80iterations 2.3899511E-03 8.3905041E-02 at 90iterations 1.0055164E-03 3.9512634E-02 at 100iterations 4.5052156E-04 1.6178131E-02 at 110iterations 2.2268556E-04 9.0675354E-03 at 120iterations finished qdiffx linear iterations at : 08:57:07 total time elapsed so far: 7.840000 # loops : 120 mean,max change (kT/e) : 2.2268556E-04 9.0675354E-03 energy calculations done at 7.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.030000 DelPhi exited at 08:57:08 8.028u 0.236s 0:08.81 93.6% 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 Wed Feb 15 2012 at 08:57:08 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5868 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 2.169027 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): -55.32700 18.53100 ymin,ymax (A): -35.61000 28.11900 zmin,zma (A): 28.96800 94.33000 x,y,z range (A): 73.85800 63.72900 65.36200 scale (grids/A): 2.169027 object centre (A): -18.39800 -3.745501 61.64900 number of atom coordinates read : 5868 total number of charged atoms : 5698 net assigned charge : -4.999963 assigned positive charge : 879.0463 centred at (gu) : 90.95393 88.82581 86.25498 assigned negative charge : -884.0535 centred at (gu) : 91.50108 88.75593 86.10999 start vw surface at 0.2300000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 226907 reading accessible surface arcs data from file ARCDAT no. of arc points read = 51768 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 97481 mr = 162965 m= 21698 mr = 74676 m= 2395 mr = 15019 m= 70 mr = 1297 m= 2 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 3184 time to turn everything in is 1.750000 number of dielectric boundary points 94590 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 143 iepsmp to db, and charging done at 1.900000 number of grid points assigned charge 45349 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) : 1.446018 object centre at (A) : -18.39800 -3.745501 61.64900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2374711 -0.1159287 midg,1,midg; midg,igrid,midg 4.6223693E-02 4.3106895E-02 1,midg,midg; igrid,midg,midg 0.1946911 -0.1744065 gauss-seidel spectral radius is 0.9991462 estimated iterations to convergence 270 setup time was (sec) 2.080000 now iterating at: 08:57:10 rms-change max change #iterations 10.60179 279.9760 at 10iterations 6.059135 163.2258 at 20iterations 3.444809 83.59199 at 30iterations 1.953185 52.00044 at 40iterations 1.099606 21.96841 at 50iterations 0.6189328 11.87766 at 60iterations 0.3472977 6.943530 at 70iterations 0.1939595 3.676584 at 80iterations 0.1083160 2.125254 at 90iterations 6.0353063E-02 1.332755 at 100iterations 3.3538729E-02 0.6352072 at 110iterations 1.8699139E-02 0.3435407 at 120iterations 1.0395836E-02 0.1913700 at 130iterations 5.7843784E-03 0.1173477 at 140iterations 3.2250599E-03 5.8860779E-02 at 150iterations 1.7911271E-03 3.4457684E-02 at 160iterations 1.0002929E-03 1.8921852E-02 at 170iterations 5.6137616E-04 1.0749817E-02 at 180iterations finished qdiffx linear iterations at : 08:57:21 total time elapsed so far: 13.04000 # loops : 180 mean,max change (kT/e) : 5.6137616E-04 1.0749817E-02 energy calculations done at 13.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.23000 DelPhi exited at 08:57:21 13.228u 0.259s 0:13.80 97.6% 0+0k 0+0io 0pf+0w