Sun Oct 9 07:03:37 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 07:03:37 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2001 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 187 has a net charge of -3.0000 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: 0.6621285 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): -24.26800 26.21300 ymin,ymax (A): -45.88700 -1.027000 zmin,zma (A): -56.02800 -2.262000 x,y,z range (A): 50.48100 44.86000 53.76600 scale (grids/A): 0.6621285 object centre (A): 0.9725008 -23.45700 -29.14500 number of atom coordinates read : 2001 total number of charged atoms : 1862 net assigned charge : -2.499987 assigned positive charge : 302.0560 centred at (gu) : 89.10477 90.40754 91.51096 assigned negative charge : -304.5561 centred at (gu) : 89.03682 90.21787 91.56724 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5789 nv = 96 ne = 84 npr = 42749 no. pairs analyzed = 42749 no. exposed pairs = 2410 no. arc points = 17303 no. surface atoms = 825 nbur = 1176 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 288 mr = 3171 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 39 time to turn everything in is 0.3000000 number of dielectric boundary points 2871 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1634 ## 143 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 6774 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8049017E-09 -2.1650663E-08 midg,1,midg; midg,igrid,midg -3.5042472E-08 2.6017700E-08 1,midg,midg; igrid,midg,midg -2.1365262E-08 3.6518868E-09 gauss-seidel spectral radius is 0.9881204 estimated iterations to convergence 75 setup time was (sec) 0.5800000 now iterating at: 07:03:38 rms-change max change #iterations 0.1561854 23.76539 at 10iterations 1.6599311E-02 2.449051 at 20iterations 1.7452633E-03 0.2591984 at 30iterations 1.8474054E-04 2.9083669E-02 at 40iterations 1.9727773E-05 3.1313896E-03 at 50iterations finished qdiffx linear iterations at : 07:03:41 total time elapsed so far: 3.840000 # loops : 50 mean,max change (kT/e) : 1.9727773E-05 3.1313896E-03 energy calculations done at 3.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.020000 DelPhi exited at 07:03:42 4.022u 0.237s 0:04.55 93.4% 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 Sun Oct 9 2011 at 07:03:42 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2001 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 187 has a net charge of -3.0000 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: 1.986385 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): -24.26800 26.21300 ymin,ymax (A): -45.88700 -1.027000 zmin,zma (A): -56.02800 -2.262000 x,y,z range (A): 50.48100 44.86000 53.76600 scale (grids/A): 1.986385 object centre (A): 0.9725008 -23.45700 -29.14500 number of atom coordinates read : 2001 total number of charged atoms : 1862 net assigned charge : -2.499987 assigned positive charge : 302.0560 centred at (gu) : 87.31453 91.22263 94.53294 assigned negative charge : -304.5561 centred at (gu) : 87.11067 90.65376 94.70184 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 62518 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17303 grid for indexing accessible points = 1.400000 m= 21809 mr = 43157 m= 3321 mr = 16159 m= 207 mr = 2032 m= 2 mr = 73 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 1314 time to turn everything in is 0.5700000 number of dielectric boundary points 26436 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 106 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 14718 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) : 0.6621285 object centre at (A) : 0.9725008 -23.45700 -29.14500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4747275E-02 -5.8706764E-02 midg,1,midg; midg,igrid,midg -3.0446235E-02 4.0008210E-02 1,midg,midg; igrid,midg,midg -4.4768337E-02 -9.8210890E-03 gauss-seidel spectral radius is 0.9986753 estimated iterations to convergence 218 setup time was (sec) 0.8700000 now iterating at: 07:03:43 rms-change max change #iterations 4.102099 192.5512 at 10iterations 1.933554 71.78092 at 20iterations 0.9135786 31.18949 at 30iterations 0.4324190 17.23711 at 40iterations 0.2049899 6.638541 at 50iterations 9.6547224E-02 3.475073 at 60iterations 4.5861118E-02 1.518242 at 70iterations 2.1769054E-02 0.7693996 at 80iterations 1.0240627E-02 0.3655968 at 90iterations 4.8725009E-03 0.1706238 at 100iterations 2.3098234E-03 7.4314117E-02 at 110iterations 1.0991301E-03 3.7696838E-02 at 120iterations finished qdiffx linear iterations at : 07:03:51 total time elapsed so far: 9.020000 # loops : 120 mean,max change (kT/e) : 1.0991301E-03 3.7696838E-02 energy calculations done at 9.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.200000 DelPhi exited at 07:03:51 9.203u 0.291s 0:09.79 96.9% 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 Sun Oct 9 2011 at 07:03:51 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: 324 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2001 !!! WARNING: ASP 186 has a net charge of -2.0000 !!! WARNING: NDP 187 has a net charge of -3.0000 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: 2.979578 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): -24.26800 26.21300 ymin,ymax (A): -45.88700 -1.027000 zmin,zma (A): -56.02800 -2.262000 x,y,z range (A): 50.48100 44.86000 53.76600 scale (grids/A): 2.979578 object centre (A): 0.9725008 -23.45700 -29.14500 number of atom coordinates read : 2001 total number of charged atoms : 1862 net assigned charge : -2.499987 assigned positive charge : 302.0560 centred at (gu) : 85.97176 91.83382 96.79938 assigned negative charge : -304.5561 centred at (gu) : 85.66603 90.98061 97.05281 start vw surface at 0.1400000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 144545 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17303 grid for indexing accessible points = 1.400000 m= 71055 mr = 104410 m= 25000 mr = 58258 m= 6102 mr = 20175 m= 919 mr = 4585 m= 58 mr = 599 m= 1 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 4527 time to turn everything in is 1.440000 number of dielectric boundary points 59628 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.580000 number of grid points assigned charge 14892 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) : 1.986385 object centre at (A) : 0.9725008 -23.45700 -29.14500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8123075 -0.8467504 midg,1,midg; midg,igrid,midg -0.3350422 0.4448240 1,midg,midg; igrid,midg,midg -0.4224041 -0.1114324 gauss-seidel spectral radius is 0.9992569 estimated iterations to convergence 290 setup time was (sec) 1.750000 now iterating at: 07:03:53 rms-change max change #iterations 9.391604 382.6741 at 10iterations 5.383223 120.5900 at 20iterations 3.101097 63.25272 at 30iterations 1.777217 35.44836 at 40iterations 1.017882 21.07570 at 50iterations 0.5836020 11.18707 at 60iterations 0.3336177 6.314242 at 70iterations 0.1917140 3.890585 at 80iterations 0.1097692 2.095327 at 90iterations 6.2863976E-02 1.219349 at 100iterations 3.5963885E-02 0.7596588 at 110iterations 2.0620279E-02 0.3697815 at 120iterations 1.1815209E-02 0.2279353 at 130iterations 6.7581902E-03 0.1248779 at 140iterations 3.8753951E-03 7.5042725E-02 at 150iterations 2.2148772E-03 4.2776585E-02 at 160iterations 1.2702951E-03 2.5943756E-02 at 170iterations 7.2822237E-04 1.4518738E-02 at 180iterations finished qdiffx linear iterations at : 07:04:07 total time elapsed so far: 15.01000 # loops : 180 mean,max change (kT/e) : 7.2822237E-04 1.4518738E-02 energy calculations done at 15.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.18000 DelPhi exited at 07:04:07 15.185u 0.311s 0:15.81 97.9% 0+0k 0+0io 0pf+0w