Sat Oct 15 14:33:52 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 Sat Oct 15 2011 at 14:33:53 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2839 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 0.6198635 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): -8.715000 48.71700 ymin,ymax (A): -8.420000 38.74900 zmin,zma (A): -0.2140000 54.41000 x,y,z range (A): 57.43200 47.16900 54.62400 scale (grids/A): 0.6198635 object centre (A): 20.00100 15.16450 27.09800 number of atom coordinates read : 2839 total number of charged atoms : 2698 net assigned charge : -4.985982 assigned positive charge : 428.7971 centred at (gu) : 88.86500 89.70856 89.17184 assigned negative charge : -433.7842 centred at (gu) : 88.82480 89.61842 89.08599 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7373 nv = 96 ne = 84 npr = 57059 no. pairs analyzed = 57059 no. exposed pairs = 3763 no. arc points = 26645 no. surface atoms = 1263 nbur = 1576 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 330 mr = 3810 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.2100000 number of dielectric boundary points 3880 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2716 ## 261 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9010 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2330196E-08 1.9737678E-09 midg,1,midg; midg,igrid,midg -1.1291806E-08 2.5390356E-09 1,midg,midg; igrid,midg,midg -8.7818952E-09 -7.4746631E-10 gauss-seidel spectral radius is 0.9865500 estimated iterations to convergence 71 setup time was (sec) 0.4300000 now iterating at: 14:33:54 rms-change max change #iterations 0.1325627 20.69933 at 10iterations 1.2408691E-02 1.673891 at 20iterations 1.1181927E-03 0.1668968 at 30iterations 1.0407606E-04 1.4655590E-02 at 40iterations 9.5232408E-06 1.3844073E-03 at 50iterations finished qdiffx linear iterations at : 14:33:59 total time elapsed so far: 3.530000 # loops : 50 mean,max change (kT/e) : 9.5232408E-06 1.3844073E-03 energy calculations done at 3.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.660000 DelPhi exited at 14:34:01 3.668u 0.233s 0:08.52 45.6% 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 Sat Oct 15 2011 at 14:34:03 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2839 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 1.859590 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): -8.715000 48.71700 ymin,ymax (A): -8.420000 38.74900 zmin,zma (A): -0.2140000 54.41000 x,y,z range (A): 57.43200 47.16900 54.62400 scale (grids/A): 1.859590 object centre (A): 20.00100 15.16450 27.09800 number of atom coordinates read : 2839 total number of charged atoms : 2698 net assigned charge : -4.985982 assigned positive charge : 428.7971 centred at (gu) : 86.59428 89.12470 87.51484 assigned negative charge : -433.7842 centred at (gu) : 86.47398 88.85480 87.25755 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 79841 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26645 grid for indexing accessible points = 1.400000 m= 26171 mr = 53738 m= 3359 mr = 18217 m= 135 mr = 1750 m= 4 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 577 time to turn everything in is 0.3800000 number of dielectric boundary points 35793 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 234 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 21184 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) : 0.6198635 object centre at (A) : 20.00100 15.16450 27.09800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2933115E-03 6.2483633E-03 midg,1,midg; midg,igrid,midg -2.1584032E-02 -2.8416403E-03 1,midg,midg; igrid,midg,midg -5.3348329E-02 2.3677746E-02 gauss-seidel spectral radius is 0.9986009 estimated iterations to convergence 212 setup time was (sec) 0.6300000 now iterating at: 14:34:07 rms-change max change #iterations 4.292332 199.8019 at 10iterations 1.984275 71.88716 at 20iterations 0.9181331 29.11308 at 30iterations 0.4251475 15.05160 at 40iterations 0.1968383 6.025218 at 50iterations 9.1140077E-02 3.328986 at 60iterations 4.2150553E-02 1.341406 at 70iterations 1.9593701E-02 0.7087126 at 80iterations 9.0723541E-03 0.3228617 at 90iterations 4.2084507E-03 0.1317024 at 100iterations 1.9523894E-03 6.6387177E-02 at 110iterations 9.0438518E-04 2.7578354E-02 at 120iterations finished qdiffx linear iterations at : 14:34:23 total time elapsed so far: 8.530000 # loops : 120 mean,max change (kT/e) : 9.0438518E-04 2.7578354E-02 energy calculations done at 8.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.670000 DelPhi exited at 14:34:24 8.676u 0.256s 0:21.15 42.1% 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 Sat Oct 15 2011 at 14:34:24 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2839 !!! WARNING: HIT 107 has a net charge of 0.5140 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: 2.789386 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): -8.715000 48.71700 ymin,ymax (A): -8.420000 38.74900 zmin,zma (A): -0.2140000 54.41000 x,y,z range (A): 57.43200 47.16900 54.62400 scale (grids/A): 2.789386 object centre (A): 20.00100 15.16450 27.09800 number of atom coordinates read : 2839 total number of charged atoms : 2698 net assigned charge : -4.985982 assigned positive charge : 428.7971 centred at (gu) : 84.89118 88.68687 86.27218 assigned negative charge : -433.7842 centred at (gu) : 84.71092 88.28214 85.88616 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 184995 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26645 grid for indexing accessible points = 1.400000 m= 87565 mr = 131432 m= 28320 mr = 69554 m= 5655 mr = 21519 m= 539 mr = 3734 m= 17 mr = 253 m= 0 mr = 4 time to grow re-entrant surface = 0.5600001 no. cavity mid-points inaccessible to solvent = 1968 time to turn everything in is 0.9900000 number of dielectric boundary points 80595 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 21581 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) : 1.859590 object centre at (A) : 20.00100 15.16450 27.09800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1541409 -0.1998543 midg,1,midg; midg,igrid,midg -0.2227245 -4.7042012E-02 1,midg,midg; igrid,midg,midg -0.6159918 0.6204816 gauss-seidel spectral radius is 0.9992678 estimated iterations to convergence 292 setup time was (sec) 1.260000 now iterating at: 14:34:25 rms-change max change #iterations 10.41074 318.1709 at 10iterations 6.161049 149.6501 at 20iterations 3.624922 79.96947 at 30iterations 2.121851 48.11045 at 40iterations 1.234160 27.57794 at 50iterations 0.7188428 13.35712 at 60iterations 0.4164516 8.415352 at 70iterations 0.2411226 4.952688 at 80iterations 0.1394269 2.743929 at 90iterations 8.0715016E-02 1.478176 at 100iterations 4.6656962E-02 0.8638792 at 110iterations 2.6880968E-02 0.5662022 at 120iterations 1.5507580E-02 0.2617378 at 130iterations 8.9532640E-03 0.1714439 at 140iterations 5.1667737E-03 0.1039829 at 150iterations 2.9749491E-03 5.9391499E-02 at 160iterations 1.7160126E-03 3.9441109E-02 at 170iterations 9.8909647E-04 1.8741369E-02 at 180iterations finished qdiffx linear iterations at : 14:34:53 total time elapsed so far: 14.33000 # loops : 180 mean,max change (kT/e) : 9.8909647E-04 1.8741369E-02 energy calculations done at 14.33000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.46000 DelPhi exited at 14:34:54 14.465u 0.252s 0:30.47 48.2% 0+0k 0+0io 0pf+0w