Tue Oct 11 06:02:19 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+sph.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 = amb.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 Tue Oct 11 2011 at 06:02:19 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7038077 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): 25.76500 72.20100 ymin,ymax (A): -18.96300 31.61900 zmin,zma (A): 4.000000 46.26600 x,y,z range (A): 46.43600 50.58200 42.26600 scale (grids/A): 0.7038077 object centre (A): 48.98300 6.328000 25.13300 number of atom coordinates read : 2327 total number of charged atoms : 2002 net assigned charge : 6.500009 assigned positive charge : 325.3439 centred at (gu) : 89.24217 90.23924 90.33622 assigned negative charge : -318.8441 centred at (gu) : 89.37085 90.19131 90.42165 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7192 nv = 96 ne = 84 npr = 42618 no. pairs analyzed = 42618 no. exposed pairs = 2585 no. arc points = 17600 no. surface atoms = 886 nbur = 1441 mkacc time = 6.9999993E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 491 mr = 4176 m= 1 mr = 87 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3421 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1609 ## 157 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7989 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.3753271E-08 1.0265841E-08 midg,1,midg; midg,igrid,midg 2.6347745E-08 7.5554873E-08 1,midg,midg; igrid,midg,midg 1.2657277E-07 -8.8716163E-09 gauss-seidel spectral radius is 0.9894812 estimated iterations to convergence 79 setup time was (sec) 0.3600000 now iterating at: 06:02:19 rms-change max change #iterations 0.1969581 35.14269 at 10iterations 2.4808625E-02 3.217883 at 20iterations 3.2820003E-03 0.3936081 at 30iterations 5.9115840E-04 7.9658508E-02 at 40iterations 1.6037148E-04 1.8829346E-02 at 50iterations finished qdiffx linear iterations at : 06:02:22 total time elapsed so far: 3.280000 # loops : 50 mean,max change (kT/e) : 1.6037148E-04 1.8829346E-02 energy calculations done at 3.280000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 06:02:23 3.414u 0.178s 0:04.57 78.3% 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 Tue Oct 11 2011 at 06:02:23 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.111423 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): 25.76500 72.20100 ymin,ymax (A): -18.96300 31.61900 zmin,zma (A): 4.000000 46.26600 x,y,z range (A): 46.43600 50.58200 42.26600 scale (grids/A): 2.111423 object centre (A): 48.98300 6.328000 25.13300 number of atom coordinates read : 2327 total number of charged atoms : 2002 net assigned charge : 6.500009 assigned positive charge : 325.3439 centred at (gu) : 87.72654 90.71744 91.00871 assigned negative charge : -318.8441 centred at (gu) : 88.11267 90.57384 91.26496 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 75904 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17600 grid for indexing accessible points = 1.400000 m= 31127 mr = 54236 m= 5959 mr = 23682 m= 541 mr = 3960 m= 19 mr = 256 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 31416 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 91 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 15888 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) : 0.7038077 object centre at (A) : 48.98300 6.328000 25.13300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.1153951E-02 2.6647709E-02 midg,1,midg; midg,igrid,midg 4.7686037E-02 2.7050052E-02 1,midg,midg; igrid,midg,midg 4.2772505E-02 -4.4222135E-02 gauss-seidel spectral radius is 0.9988247 estimated iterations to convergence 231 setup time was (sec) 0.6100000 now iterating at: 06:02:24 rms-change max change #iterations 4.605786 189.5620 at 10iterations 2.272638 76.94059 at 20iterations 1.123679 36.14046 at 30iterations 0.5583192 16.74637 at 40iterations 0.2764755 10.17014 at 50iterations 0.1372557 4.177327 at 60iterations 6.8018392E-02 2.161430 at 70iterations 3.3739142E-02 1.160285 at 80iterations 1.6874328E-02 0.5726166 at 90iterations 8.4225191E-03 0.2430463 at 100iterations 4.2275595E-03 0.1269569 at 110iterations 2.1858346E-03 6.4662933E-02 at 120iterations finished qdiffx linear iterations at : 06:02:31 total time elapsed so far: 7.830000 # loops : 120 mean,max change (kT/e) : 2.1858346E-03 6.4662933E-02 energy calculations done at 7.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.950000 DelPhi exited at 06:02:32 7.956u 0.231s 0:08.58 95.3% 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 Tue Oct 11 2011 at 06:02:32 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.167135 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): 25.76500 72.20100 ymin,ymax (A): -18.96300 31.61900 zmin,zma (A): 4.000000 46.26600 x,y,z range (A): 46.43600 50.58200 42.26600 scale (grids/A): 3.167135 object centre (A): 48.98300 6.328000 25.13300 number of atom coordinates read : 2327 total number of charged atoms : 2002 net assigned charge : 6.500009 assigned positive charge : 325.3439 centred at (gu) : 86.58974 91.07629 91.51310 assigned negative charge : -318.8441 centred at (gu) : 87.16898 90.86069 91.89749 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 174771 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17600 grid for indexing accessible points = 1.400000 m= 96422 mr = 130200 m= 39635 mr = 80442 m= 11193 mr = 32660 m= 2117 mr = 8664 m= 246 mr = 1512 m= 20 mr = 139 m= 0 mr = 8 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.180000 number of dielectric boundary points 70779 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.270000 number of grid points assigned charge 16016 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) : 2.111423 object centre at (A) : 48.98300 6.328000 25.13300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1258279 0.2250864 midg,1,midg; midg,igrid,midg 0.3790434 0.1202050 1,midg,midg; igrid,midg,midg 0.4280214 -0.5461926 gauss-seidel spectral radius is 0.9992962 estimated iterations to convergence 297 setup time was (sec) 1.400000 now iterating at: 06:02:33 rms-change max change #iterations 10.36458 346.7103 at 10iterations 6.136588 182.9279 at 20iterations 3.633787 75.44048 at 30iterations 2.141185 41.24146 at 40iterations 1.260322 25.19318 at 50iterations 0.7411712 14.36913 at 60iterations 0.4353610 7.724606 at 70iterations 0.2549509 4.743351 at 80iterations 0.1496116 2.626232 at 90iterations 8.7750830E-02 1.628454 at 100iterations 5.1512700E-02 1.014816 at 110iterations 3.0270783E-02 0.5240269 at 120iterations 1.7841727E-02 0.3175354 at 130iterations 1.0668444E-02 0.1916599 at 140iterations 6.4601311E-03 0.1408424 at 150iterations 4.0143081E-03 7.8376770E-02 at 160iterations 2.6144315E-03 5.4069519E-02 at 170iterations 1.7982904E-03 3.5285950E-02 at 180iterations finished qdiffx linear iterations at : 06:02:45 total time elapsed so far: 12.62000 # loops : 180 mean,max change (kT/e) : 1.7982904E-03 3.5285950E-02 energy calculations done at 12.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.75000 DelPhi exited at 06:02:46 12.750u 0.220s 0:13.88 93.4% 0+0k 0+0io 0pf+0w