Sat Oct 8 16:13:43 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 8 2011 at 16:13:43 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2446 !!! WARNING: ASL 35 has a net charge of -0.1000 !!! WARNING: GLM 41 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6255491 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): -2.423000 45.00900 ymin,ymax (A): -15.38900 29.74400 zmin,zma (A): -18.69900 38.21100 x,y,z range (A): 47.43200 45.13300 56.91000 scale (grids/A): 0.6255491 object centre (A): 21.29300 7.177500 9.756001 number of atom coordinates read : 2446 total number of charged atoms : 2383 net assigned charge : 1.806002 assigned positive charge : 368.7458 centred at (gu) : 91.24042 88.62890 90.04206 assigned negative charge : -366.9408 centred at (gu) : 91.34312 88.78046 90.15501 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6496 nv = 96 ne = 84 npr = 48281 no. pairs analyzed = 48281 no. exposed pairs = 3188 no. arc points = 21726 no. surface atoms = 1086 nbur = 1360 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 355 mr = 3585 m= 0 mr = 46 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3220 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2152 ## 223 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 7981 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.7748956E-09 -6.7997230E-09 midg,1,midg; midg,igrid,midg 1.7132347E-08 -7.1104793E-09 1,midg,midg; igrid,midg,midg 6.9605930E-09 -7.9149505E-09 gauss-seidel spectral radius is 0.9867537 estimated iterations to convergence 71 setup time was (sec) 0.4700000 now iterating at: 16:13:44 rms-change max change #iterations 0.1280283 19.21866 at 10iterations 1.1947995E-02 1.768108 at 20iterations 1.1694561E-03 0.1796227 at 30iterations 1.3532263E-04 2.1102905E-02 at 40iterations 2.5418163E-05 3.7331581E-03 at 50iterations finished qdiffx linear iterations at : 16:13:46 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 2.5418163E-05 3.7331581E-03 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 16:13:47 3.089u 0.158s 0:03.53 91.5% 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 Sat Oct 8 2011 at 16:13:47 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2446 !!! WARNING: ASL 35 has a net charge of -0.1000 !!! WARNING: GLM 41 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.876647 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): -2.423000 45.00900 ymin,ymax (A): -15.38900 29.74400 zmin,zma (A): -18.69900 38.21100 x,y,z range (A): 47.43200 45.13300 56.91000 scale (grids/A): 1.876647 object centre (A): 21.29300 7.177500 9.756001 number of atom coordinates read : 2446 total number of charged atoms : 2383 net assigned charge : 1.806002 assigned positive charge : 368.7458 centred at (gu) : 93.72081 85.88620 90.12539 assigned negative charge : -366.9408 centred at (gu) : 94.02907 86.34128 90.46484 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 70750 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21726 grid for indexing accessible points = 1.400000 m= 24459 mr = 49219 m= 3822 mr = 17645 m= 205 mr = 2405 m= 1 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 228 time to turn everything in is 0.5000000 number of dielectric boundary points 29909 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 165 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 18713 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) : 0.6255491 object centre at (A) : 21.29300 7.177500 9.756001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6911030E-02 -2.0367520E-02 midg,1,midg; midg,igrid,midg 2.6021445E-02 -5.1572495E-03 1,midg,midg; igrid,midg,midg 5.2223057E-03 -4.1695692E-02 gauss-seidel spectral radius is 0.9985833 estimated iterations to convergence 211 setup time was (sec) 0.7700000 now iterating at: 16:13:48 rms-change max change #iterations 4.034783 215.4105 at 10iterations 1.848050 74.63562 at 20iterations 0.8617517 28.92295 at 30iterations 0.3971386 12.63434 at 40iterations 0.1836361 6.169678 at 50iterations 8.4842317E-02 2.846956 at 60iterations 3.9242193E-02 1.345710 at 70iterations 1.8146953E-02 0.5767288 at 80iterations 8.4035657E-03 0.2845521 at 90iterations 3.8863909E-03 0.1342058 at 100iterations 1.7992203E-03 6.1064720E-02 at 110iterations 8.3651743E-04 2.6344299E-02 at 120iterations finished qdiffx linear iterations at : 16:13:54 total time elapsed so far: 6.790000 # loops : 120 mean,max change (kT/e) : 8.3651743E-04 2.6344299E-02 energy calculations done at 6.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.970000 DelPhi exited at 16:13:54 6.969u 0.184s 0:07.48 95.4% 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 8 2011 at 16:13:54 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2446 !!! WARNING: ASL 35 has a net charge of -0.1000 !!! WARNING: GLM 41 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.814971 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): -2.423000 45.00900 ymin,ymax (A): -15.38900 29.74400 zmin,zma (A): -18.69900 38.21100 x,y,z range (A): 47.43200 45.13300 56.91000 scale (grids/A): 2.814971 object centre (A): 21.29300 7.177500 9.756001 number of atom coordinates read : 2446 total number of charged atoms : 2383 net assigned charge : 1.806002 assigned positive charge : 368.7458 centred at (gu) : 95.58101 83.82906 90.18793 assigned negative charge : -366.9408 centred at (gu) : 96.04362 84.51189 90.69719 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 163825 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21726 grid for indexing accessible points = 1.400000 m= 80470 mr = 119545 m= 28100 mr = 65184 m= 6875 mr = 22392 m= 905 mr = 5099 m= 45 mr = 553 m= 1 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 850 time to turn everything in is 1.230000 number of dielectric boundary points 67424 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 19063 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) : 1.876647 object centre at (A) : 21.29300 7.177500 9.756001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1811239 -0.2658965 midg,1,midg; midg,igrid,midg 0.2394982 -6.1217148E-02 1,midg,midg; igrid,midg,midg 3.9804034E-02 -0.5403469 gauss-seidel spectral radius is 0.9992462 estimated iterations to convergence 287 setup time was (sec) 1.510000 now iterating at: 16:13:56 rms-change max change #iterations 9.605715 303.0535 at 10iterations 5.667397 133.2934 at 20iterations 3.301429 70.91195 at 30iterations 1.924389 42.80882 at 40iterations 1.113063 21.80874 at 50iterations 0.6436658 13.28620 at 60iterations 0.3708693 7.026081 at 70iterations 0.2131281 4.306148 at 80iterations 0.1228664 2.294599 at 90iterations 7.0527382E-02 1.276413 at 100iterations 4.0445793E-02 0.7163239 at 110iterations 2.3145622E-02 0.4223628 at 120iterations 1.3271249E-02 0.2483990 at 130iterations 7.6171793E-03 0.1575413 at 140iterations 4.3558893E-03 8.1842422E-02 at 150iterations 2.4987631E-03 4.5750380E-02 at 160iterations 1.4298363E-03 2.8366089E-02 at 170iterations 8.2405057E-04 1.5766144E-02 at 180iterations finished qdiffx linear iterations at : 16:14:06 total time elapsed so far: 10.92000 # loops : 180 mean,max change (kT/e) : 8.2405057E-04 1.5766144E-02 energy calculations done at 10.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.09000 DelPhi exited at 16:14:06 11.092u 0.213s 0:11.62 97.2% 0+0k 0+0io 0pf+0w