Mon Oct 10 17:04:23 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 17:04:23 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4692 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 0.5145550 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): -17.87500 36.03300 ymin,ymax (A): -30.58000 33.92900 zmin,zma (A): -3.917000 65.26900 x,y,z range (A): 53.90800 64.50900 69.18600 scale (grids/A): 0.5145550 object centre (A): 9.079000 1.674500 30.67600 number of atom coordinates read : 4692 total number of charged atoms : 4443 net assigned charge : 7.206037 assigned positive charge : 703.7957 centred at (gu) : 90.46126 90.28593 88.19823 assigned negative charge : -696.5940 centred at (gu) : 90.36304 90.34977 88.17014 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 7782 nv = 96 ne = 84 npr = 95187 no. pairs analyzed = 95187 no. exposed pairs = 5986 no. arc points = 41365 no. surface atoms = 2006 nbur = 2686 mkacc time = 0.2200000 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 = 1.652000 m= 279 mr = 3988 m= 0 mr = 3 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4700000 number of dielectric boundary points 4070 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3952 ## 585 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 10377 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.7920297E-11 1.2968060E-10 midg,1,midg; midg,igrid,midg 2.8862299E-10 -7.5514137E-11 1,midg,midg; igrid,midg,midg -1.5359228E-10 4.6424475E-10 gauss-seidel spectral radius is 0.9806772 estimated iterations to convergence 59 setup time was (sec) 0.7200000 now iterating at: 17:04:24 rms-change max change #iterations 7.0064552E-02 9.841690 at 10iterations 4.0960545E-03 0.6144276 at 20iterations 3.6620791E-04 5.4805279E-02 at 30iterations 1.1192457E-04 1.7391205E-02 at 40iterations 4.5491422E-05 7.0834160E-03 at 50iterations finished qdiffx linear iterations at : 17:04:27 total time elapsed so far: 3.590000 # loops : 50 mean,max change (kT/e) : 4.5491422E-05 7.0834160E-03 energy calculations done at 3.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.810000 DelPhi exited at 17:04:28 3.814u 0.214s 0:04.93 81.5% 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 Mon Oct 10 2011 at 17:04:28 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4692 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 1.543665 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): -17.87500 36.03300 ymin,ymax (A): -30.58000 33.92900 zmin,zma (A): -3.917000 65.26900 x,y,z range (A): 53.90800 64.50900 69.18600 scale (grids/A): 1.543665 object centre (A): 9.079000 1.674500 30.67600 number of atom coordinates read : 4692 total number of charged atoms : 4443 net assigned charge : 7.206037 assigned positive charge : 703.7957 centred at (gu) : 91.38226 90.85640 84.59345 assigned negative charge : -696.5940 centred at (gu) : 91.08872 91.04904 84.51006 start vw surface at 0.2100000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 87679 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41365 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 25199 mr = 59660 m= 2288 mr = 16697 m= 48 mr = 969 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6700000 number of dielectric boundary points 37888 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 528 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 33445 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) : 0.5145550 object centre at (A) : 9.079000 1.674500 30.67600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6798523E-03 1.9222230E-02 midg,1,midg; midg,igrid,midg 9.8376507E-03 -1.0874249E-02 1,midg,midg; igrid,midg,midg -1.1143810E-03 1.0854947E-02 gauss-seidel spectral radius is 0.9981371 estimated iterations to convergence 184 setup time was (sec) 0.9900000 now iterating at: 17:04:29 rms-change max change #iterations 3.834434 149.7479 at 10iterations 1.580789 54.00903 at 20iterations 0.6519540 22.34077 at 30iterations 0.2689017 8.810566 at 40iterations 0.1111046 3.585159 at 50iterations 4.6063513E-02 1.479057 at 60iterations 1.8960305E-02 0.6033592 at 70iterations 7.8364927E-03 0.2550697 at 80iterations 3.2479120E-03 0.1002898 at 90iterations 1.3446439E-03 4.0375710E-02 at 100iterations 5.5703946E-04 1.8805504E-02 at 110iterations 2.3025359E-04 7.7743530E-03 at 120iterations finished qdiffx linear iterations at : 17:04:37 total time elapsed so far: 8.790000 # loops : 120 mean,max change (kT/e) : 2.3025359E-04 7.7743530E-03 energy calculations done at 8.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.980000 DelPhi exited at 17:04:38 8.982u 0.261s 0:10.39 88.9% 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 Mon Oct 10 2011 at 17:04:38 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: 312 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4692 !!! WARNING: GLM 169 has a net charge of -0.0940 !!! WARNING: HEM 819 has a net charge of 1.4000 !!! WARNING: FE 3 has a net charge of 1.4000 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: 2.315497 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): -17.87500 36.03300 ymin,ymax (A): -30.58000 33.92900 zmin,zma (A): -3.917000 65.26900 x,y,z range (A): 53.90800 64.50900 69.18600 scale (grids/A): 2.315497 object centre (A): 9.079000 1.674500 30.67600 number of atom coordinates read : 4692 total number of charged atoms : 4443 net assigned charge : 7.206037 assigned positive charge : 703.7957 centred at (gu) : 92.07301 91.28425 81.88982 assigned negative charge : -696.5940 centred at (gu) : 91.63307 91.57348 81.76502 start vw surface at 0.2200000 fill in re-entrant regions at 0.5700000 boundary points on vw surface= 204254 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41365 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 90183 mr = 146611 m= 22882 mr = 70099 m= 3314 mr = 16331 m= 191 mr = 2036 m= 1 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 0.9200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.600000 number of dielectric boundary points 85671 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 72 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 35462 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) : 1.543665 object centre at (A) : 9.079000 1.674500 30.67600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1515825 0.4567718 midg,1,midg; midg,igrid,midg 0.1011127 -0.2773019 1,midg,midg; igrid,midg,midg -1.2611329E-02 0.1608903 gauss-seidel spectral radius is 0.9991680 estimated iterations to convergence 274 setup time was (sec) 1.930000 now iterating at: 17:04:40 rms-change max change #iterations 10.26031 325.7159 at 10iterations 5.879271 126.8768 at 20iterations 3.347340 70.66595 at 30iterations 1.895300 46.43655 at 40iterations 1.071357 23.45578 at 50iterations 0.6018823 12.38165 at 60iterations 0.3381510 7.522396 at 70iterations 0.1895224 4.023560 at 80iterations 0.1058767 2.089316 at 90iterations 5.9289794E-02 1.189801 at 100iterations 3.3072907E-02 0.6286240 at 110iterations 1.8465629E-02 0.3893352 at 120iterations 1.0290085E-02 0.1920010 at 130iterations 5.7446575E-03 0.1121492 at 140iterations 3.1974853E-03 6.2896252E-02 at 150iterations 1.7817735E-03 3.4355164E-02 at 160iterations 9.9416031E-04 1.9802094E-02 at 170iterations 5.5661739E-04 1.0623932E-02 at 180iterations finished qdiffx linear iterations at : 17:04:54 total time elapsed so far: 15.46000 # loops : 180 mean,max change (kT/e) : 5.5661739E-04 1.0623932E-02 energy calculations done at 15.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.65000 DelPhi exited at 17:04:55 15.656u 0.212s 0:16.77 94.5% 0+0k 0+0io 0pf+0w