Sun Oct 9 08:18:32 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 Sun Oct 9 2011 at 08:18:32 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5951 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1800000 grid size : 179 scale,in grids/A, set to be: 0.4805162 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): -32.59400 26.91600 ymin,ymax (A): -13.45100 60.63600 zmin,zma (A): -28.62100 41.76300 x,y,z range (A): 59.51000 74.08700 70.38400 scale (grids/A): 0.4805162 object centre (A): -2.839001 23.59250 6.571000 number of atom coordinates read : 5951 total number of charged atoms : 5782 net assigned charge : -0.4999603 assigned positive charge : 893.5119 centred at (gu) : 88.40860 89.60245 89.58660 assigned negative charge : -894.0197 centred at (gu) : 88.40224 89.43105 89.59301 start vw surface at 0.2800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 8463 nv = 96 ne = 84 npr = 120920 no. pairs analyzed = 120920 no. exposed pairs = 7300 no. arc points = 50561 no. surface atoms = 2462 nbur = 3489 mkacc time = 0.3500000 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 = 1.764000 m= 239 mr = 4320 m= 0 mr = 2 time to grow re-entrant surface = 0.3799999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6900000 number of dielectric boundary points 4380 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4810 ## 838 charges are in solution ## iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 11595 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.9477258E-12 -5.5098799E-12 midg,1,midg; midg,igrid,midg -1.6322919E-10 1.2261851E-10 1,midg,midg; igrid,midg,midg -9.6222075E-12 2.7637450E-12 gauss-seidel spectral radius is 0.9779432 estimated iterations to convergence 56 setup time was (sec) 1.000000 now iterating at: 08:18:34 rms-change max change #iterations 5.5349905E-02 10.36290 at 10iterations 2.6682476E-03 0.4545290 at 20iterations 1.3546027E-04 2.2323608E-02 at 30iterations 1.2470890E-05 2.3517609E-03 at 40iterations 2.8156392E-06 5.1498413E-04 at 50iterations finished qdiffx linear iterations at : 08:18:37 total time elapsed so far: 4.460000 # loops : 50 mean,max change (kT/e) : 2.8156392E-06 5.1498413E-04 energy calculations done at 4.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.700000 DelPhi exited at 08:18:38 4.705u 0.249s 0:05.23 94.4% 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 08:18:38 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5951 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1800000 grid size : 179 scale,in grids/A, set to be: 1.441548 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): -32.59400 26.91600 ymin,ymax (A): -13.45100 60.63600 zmin,zma (A): -28.62100 41.76300 x,y,z range (A): 59.51000 74.08700 70.38400 scale (grids/A): 1.441548 object centre (A): -2.839001 23.59250 6.571000 number of atom coordinates read : 5951 total number of charged atoms : 5782 net assigned charge : -0.4999603 assigned positive charge : 893.5119 centred at (gu) : 85.22371 88.80557 88.75766 assigned negative charge : -894.0197 centred at (gu) : 85.20619 88.29290 88.77859 start vw surface at 0.3000000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 98079 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50561 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.652000 m= 25441 mr = 67574 m= 1604 mr = 16141 m= 25 mr = 508 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 319 time to turn everything in is 0.9200000 number of dielectric boundary points 40926 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 850 ## 16 charges are in solution ## iepsmp to db, and charging done at 1.080000 number of grid points assigned charge 42468 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) : 0.4805162 object centre at (A) : -2.839001 23.59250 6.571000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.7956198E-03 1.5738925E-03 midg,1,midg; midg,igrid,midg -2.4358416E-03 2.1686947E-02 1,midg,midg; igrid,midg,midg -6.6211203E-04 -3.6053802E-04 gauss-seidel spectral radius is 0.9979399 estimated iterations to convergence 175 setup time was (sec) 1.310000 now iterating at: 08:18:39 rms-change max change #iterations 3.718017 131.5332 at 10iterations 1.466302 54.47398 at 20iterations 0.5779949 19.21677 at 30iterations 0.2284330 7.344589 at 40iterations 9.0038083E-02 2.729522 at 50iterations 3.5587784E-02 1.209120 at 60iterations 1.4027187E-02 0.4485931 at 70iterations 5.5813617E-03 0.1902885 at 80iterations 2.2181608E-03 7.4001312E-02 at 90iterations 8.8417094E-04 2.7911186E-02 at 100iterations 3.5831612E-04 1.1505127E-02 at 110iterations 1.5057634E-04 5.4922104E-03 at 120iterations finished qdiffx linear iterations at : 08:18:48 total time elapsed so far: 9.900000 # loops : 120 mean,max change (kT/e) : 1.5057634E-04 5.4922104E-03 energy calculations done at 9.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.13000 DelPhi exited at 08:18:48 10.136u 0.265s 0:10.71 97.0% 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 08:18:48 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5951 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1900000 grid size : 179 scale,in grids/A, set to be: 2.162323 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): -32.59400 26.91600 ymin,ymax (A): -13.45100 60.63600 zmin,zma (A): -28.62100 41.76300 x,y,z range (A): 59.51000 74.08700 70.38400 scale (grids/A): 2.162323 object centre (A): -2.839001 23.59250 6.571000 number of atom coordinates read : 5951 total number of charged atoms : 5782 net assigned charge : -0.4999603 assigned positive charge : 893.5119 centred at (gu) : 82.83515 88.20819 88.13603 assigned negative charge : -894.0197 centred at (gu) : 82.80920 87.43929 88.16774 start vw surface at 0.2800000 fill in re-entrant regions at 0.7100000 boundary points on vw surface= 229754 reading accessible surface arcs data from file ARCDAT no. of arc points read = 50561 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 96100 mr = 167391 m= 20144 mr = 73674 m= 1959 mr = 13614 m= 58 mr = 976 m= 0 mr = 9 time to grow re-entrant surface = 1.230000 no. cavity mid-points inaccessible to solvent = 1148 time to turn everything in is 2.110000 number of dielectric boundary points 92351 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 154 iepsmp to db, and charging done at 2.300000 number of grid points assigned charge 45978 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) : 1.441548 object centre at (A) : -2.839001 23.59250 6.571000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1681858 6.2561622E-03 midg,1,midg; midg,igrid,midg 0.1243926 0.6302338 1,midg,midg; igrid,midg,midg 3.5512730E-02 5.9020752E-03 gauss-seidel spectral radius is 0.9991406 estimated iterations to convergence 269 setup time was (sec) 2.530000 now iterating at: 08:18:51 rms-change max change #iterations 10.63696 288.1307 at 10iterations 6.077628 146.8688 at 20iterations 3.462877 80.65844 at 30iterations 1.958077 42.19496 at 40iterations 1.101088 23.21848 at 50iterations 0.6190481 14.21943 at 60iterations 0.3476495 6.689524 at 70iterations 0.1938871 3.646685 at 80iterations 0.1078121 2.268622 at 90iterations 6.0044721E-02 0.9985042 at 100iterations 3.3394918E-02 0.6706505 at 110iterations 1.8555708E-02 0.3295174 at 120iterations 1.0288171E-02 0.2000608 at 130iterations 5.7067079E-03 0.1046362 at 140iterations 3.1666034E-03 5.9480339E-02 at 150iterations 1.7532998E-03 3.3081055E-02 at 160iterations 9.7108027E-04 1.8766880E-02 at 170iterations 5.3904095E-04 9.8762512E-03 at 180iterations finished qdiffx linear iterations at : 08:19:05 total time elapsed so far: 16.79000 # loops : 180 mean,max change (kT/e) : 5.3904095E-04 9.8762512E-03 energy calculations done at 16.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.02000 DelPhi exited at 08:19:06 17.024u 0.319s 0:17.67 98.0% 0+0k 0+0io 0pf+0w