Mon Oct 10 16:03:24 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 Mon Oct 10 2011 at 16:03:24 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4764 !!! WARNING: GLM 134 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5408525 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): 7.681000 62.90600 ymin,ymax (A): -34.79600 29.53900 zmin,zma (A): -35.38500 30.43700 x,y,z range (A): 55.22500 64.33500 65.82201 scale (grids/A): 0.5408525 object centre (A): 35.29350 -2.628501 -2.474001 number of atom coordinates read : 4764 total number of charged atoms : 4602 net assigned charge : 6.906020 assigned positive charge : 719.6328 centred at (gu) : 89.51562 90.02910 91.16904 assigned negative charge : -712.7310 centred at (gu) : 89.50012 90.07253 91.16241 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 8837 nv = 96 ne = 84 npr = 98050 no. pairs analyzed = 98050 no. exposed pairs = 5821 no. arc points = 39205 no. surface atoms = 1954 nbur = 2810 mkacc time = 0.2100000 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 = 1.596000 m= 328 mr = 4802 m= 2 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4700000 number of dielectric boundary points 4352 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3923 ## 499 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 11770 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.2137342E-10 5.4474492E-10 midg,1,midg; midg,igrid,midg 7.2412076E-10 -3.2579599E-11 1,midg,midg; igrid,midg,midg 2.4044061E-10 4.3189802E-10 gauss-seidel spectral radius is 0.9825039 estimated iterations to convergence 62 setup time was (sec) 0.6700000 now iterating at: 16:03:25 rms-change max change #iterations 9.2559859E-02 12.93242 at 10iterations 6.8532843E-03 0.9580765 at 20iterations 1.4437368E-03 0.2327385 at 30iterations 5.9857965E-04 8.2424164E-02 at 40iterations 2.6716097E-04 3.4708023E-02 at 50iterations finished qdiffx linear iterations at : 16:03:28 total time elapsed so far: 3.130000 # loops : 50 mean,max change (kT/e) : 2.6716097E-04 3.4708023E-02 energy calculations done at 3.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 16:03:28 3.302u 0.185s 0:03.84 90.6% 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 Mon Oct 10 2011 at 16:03:28 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4764 !!! WARNING: GLM 134 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= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.622558 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): 7.681000 62.90600 ymin,ymax (A): -34.79600 29.53900 zmin,zma (A): -35.38500 30.43700 x,y,z range (A): 55.22500 64.33500 65.82201 scale (grids/A): 1.622558 object centre (A): 35.29350 -2.628501 -2.474001 number of atom coordinates read : 4764 total number of charged atoms : 4602 net assigned charge : 6.906020 assigned positive charge : 719.6328 centred at (gu) : 88.54523 90.08577 93.50575 assigned negative charge : -712.7310 centred at (gu) : 88.50007 90.21722 93.48624 start vw surface at 0.2000000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 99824 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39205 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 31063 mr = 70700 m= 3165 mr = 21483 m= 69 mr = 1599 m= 0 mr = 4 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 711 time to turn everything in is 0.6700000 number of dielectric boundary points 40335 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 421 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 35157 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) : 0.5408525 object centre at (A) : 35.29350 -2.628501 -2.474001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.5806583E-03 1.4314193E-02 midg,1,midg; midg,igrid,midg 1.2218434E-02 1.5778607E-02 1,midg,midg; igrid,midg,midg 3.2217740E-03 6.1446675E-03 gauss-seidel spectral radius is 0.9983351 estimated iterations to convergence 195 setup time was (sec) 0.9400000 now iterating at: 16:03:29 rms-change max change #iterations 4.299030 147.9724 at 10iterations 1.853485 57.87946 at 20iterations 0.8049207 25.24964 at 30iterations 0.3491241 10.71428 at 40iterations 0.1506660 4.620623 at 50iterations 6.5600850E-02 2.015942 at 60iterations 2.8665278E-02 0.8683562 at 70iterations 1.2609633E-02 0.3611336 at 80iterations 5.7131858E-03 0.1663895 at 90iterations 2.7367757E-03 8.7783813E-02 at 100iterations 1.4626819E-03 4.7015190E-02 at 110iterations 9.0704928E-04 2.6822567E-02 at 120iterations finished qdiffx linear iterations at : 16:03:35 total time elapsed so far: 7.100000 # loops : 120 mean,max change (kT/e) : 9.0704928E-04 2.6822567E-02 energy calculations done at 7.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.290000 DelPhi exited at 16:03:36 7.288u 0.195s 0:08.01 93.2% 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 Mon Oct 10 2011 at 16:03:36 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: 320 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4764 !!! WARNING: GLM 134 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.433836 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): 7.681000 62.90600 ymin,ymax (A): -34.79600 29.53900 zmin,zma (A): -35.38500 30.43700 x,y,z range (A): 55.22500 64.33500 65.82201 scale (grids/A): 2.433836 object centre (A): 35.29350 -2.628501 -2.474001 number of atom coordinates read : 4764 total number of charged atoms : 4602 net assigned charge : 6.906020 assigned positive charge : 719.6328 centred at (gu) : 87.81730 90.12830 95.25830 assigned negative charge : -712.7310 centred at (gu) : 87.74998 90.32562 95.22924 start vw surface at 0.1900000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 232506 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39205 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 108442 mr = 173218 m= 30746 mr = 86132 m= 5066 mr = 23196 m= 358 mr = 3317 m= 6 mr = 160 m= 0 mr = 0 time to grow re-entrant surface = 0.9600000 no. cavity mid-points inaccessible to solvent = 2386 time to turn everything in is 1.610000 number of dielectric boundary points 91101 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 31 iepsmp to db, and charging done at 1.750000 number of grid points assigned charge 36768 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) : 1.622558 object centre at (A) : 35.29350 -2.628501 -2.474001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.1213860E-02 0.3703984 midg,1,midg; midg,igrid,midg 0.1535867 0.3570489 1,midg,midg; igrid,midg,midg 4.9446315E-02 0.1009978 gauss-seidel spectral radius is 0.9992240 estimated iterations to convergence 283 setup time was (sec) 1.910000 now iterating at: 16:03:38 rms-change max change #iterations 11.24698 346.3444 at 10iterations 6.589053 149.7512 at 20iterations 3.850315 90.29855 at 30iterations 2.235527 43.81713 at 40iterations 1.290880 23.40510 at 50iterations 0.7424413 13.93150 at 60iterations 0.4265547 7.707302 at 70iterations 0.2443373 4.506357 at 80iterations 0.1399321 2.472281 at 90iterations 7.9955786E-02 1.364744 at 100iterations 4.5823146E-02 0.8754933 at 110iterations 2.6201712E-02 0.4687271 at 120iterations 1.5031293E-02 0.2797737 at 130iterations 8.6855339E-03 0.1562424 at 140iterations 5.0978484E-03 9.9481106E-02 at 150iterations 3.0633588E-03 5.3909302E-02 at 160iterations 1.9308070E-03 3.5865784E-02 at 170iterations 1.2990243E-03 2.4147034E-02 at 180iterations finished qdiffx linear iterations at : 16:03:49 total time elapsed so far: 12.30000 # loops : 180 mean,max change (kT/e) : 1.2990243E-03 2.4147034E-02 energy calculations done at 12.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.47000 DelPhi exited at 16:03:49 12.476u 0.220s 0:12.98 97.7% 0+0k 0+0io 0pf+0w