Sat Oct 8 22:45:47 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 Sat Oct 8 2011 at 22:45:47 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2282 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6514300 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): -29.16700 22.17200 ymin,ymax (A): 27.56500 70.70300 zmin,zma (A): -13.56100 41.08800 x,y,z range (A): 51.33900 43.13799 54.64900 scale (grids/A): 0.6514300 object centre (A): -3.497500 49.13400 13.76350 number of atom coordinates read : 2282 total number of charged atoms : 2148 net assigned charge : 11.50002 assigned positive charge : 331.9476 centred at (gu) : 91.40702 91.52459 89.48511 assigned negative charge : -320.4482 centred at (gu) : 91.41884 91.43488 89.45731 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6804 nv = 96 ne = 84 npr = 44783 no. pairs analyzed = 44783 no. exposed pairs = 3117 no. arc points = 22450 no. surface atoms = 1046 nbur = 1236 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 407 mr = 3487 m= 3 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3678 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2218 ## 204 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7829 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.1328120E-08 2.3829353E-08 midg,1,midg; midg,igrid,midg 8.2993594E-09 4.7335622E-08 1,midg,midg; igrid,midg,midg 1.8360039E-08 2.8396894E-08 gauss-seidel spectral radius is 0.9877724 estimated iterations to convergence 74 setup time was (sec) 0.4800000 now iterating at: 22:45:47 rms-change max change #iterations 0.1422186 24.42268 at 10iterations 1.4611598E-02 2.285233 at 20iterations 1.5869739E-03 0.2482166 at 30iterations 2.1856974E-04 3.9352417E-02 at 40iterations 4.2300366E-05 8.6250305E-03 at 50iterations finished qdiffx linear iterations at : 22:45:50 total time elapsed so far: 2.920000 # loops : 50 mean,max change (kT/e) : 4.2300366E-05 8.6250305E-03 energy calculations done at 2.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 22:45:50 3.092u 0.162s 0:03.54 91.8% 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 22:45:50 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 = 2282 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: 1.954290 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): -29.16700 22.17200 ymin,ymax (A): 27.56500 70.70300 zmin,zma (A): -13.56100 41.08800 x,y,z range (A): 51.33900 43.13799 54.64900 scale (grids/A): 1.954290 object centre (A): -3.497500 49.13400 13.76350 number of atom coordinates read : 2282 total number of charged atoms : 2148 net assigned charge : 11.50002 assigned positive charge : 331.9476 centred at (gu) : 94.22071 94.57359 88.45526 assigned negative charge : -320.4482 centred at (gu) : 94.25671 94.30474 88.37212 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 72212 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22450 grid for indexing accessible points = 1.400000 m= 27273 mr = 47935 m= 4958 mr = 19799 m= 360 mr = 3034 m= 7 mr = 135 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5400000 number of dielectric boundary points 33907 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 157 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 16950 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) : 0.6514300 object centre at (A) : -3.497500 49.13400 13.76350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1847704E-02 5.2610625E-02 midg,1,midg; midg,igrid,midg -5.2454756E-03 3.1281821E-02 1,midg,midg; igrid,midg,midg 5.9093140E-02 3.3892300E-02 gauss-seidel spectral radius is 0.9986838 estimated iterations to convergence 218 setup time was (sec) 0.8500000 now iterating at: 22:45:51 rms-change max change #iterations 4.035673 183.1144 at 10iterations 1.910863 68.04127 at 20iterations 0.9033237 38.91198 at 30iterations 0.4266931 13.39167 at 40iterations 0.2023453 6.155617 at 50iterations 9.5949717E-02 2.957870 at 60iterations 4.5577541E-02 1.472681 at 70iterations 2.1583704E-02 0.6930845 at 80iterations 1.0249723E-02 0.3286693 at 90iterations 4.8703770E-03 0.1570854 at 100iterations 2.3291351E-03 7.5546265E-02 at 110iterations 1.1100428E-03 3.9125443E-02 at 120iterations finished qdiffx linear iterations at : 22:45:59 total time elapsed so far: 8.080000 # loops : 120 mean,max change (kT/e) : 1.1100428E-03 3.9125443E-02 energy calculations done at 8.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.250000 DelPhi exited at 22:45:59 8.254u 0.265s 0:08.85 96.1% 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 22:45:59 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 = 2282 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: 2.931435 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): -29.16700 22.17200 ymin,ymax (A): 27.56500 70.70300 zmin,zma (A): -13.56100 41.08800 x,y,z range (A): 51.33900 43.13799 54.64900 scale (grids/A): 2.931435 object centre (A): -3.497500 49.13400 13.76350 number of atom coordinates read : 2282 total number of charged atoms : 2148 net assigned charge : 11.50002 assigned positive charge : 331.9476 centred at (gu) : 96.33115 96.86021 87.68287 assigned negative charge : -320.4482 centred at (gu) : 96.38511 96.45714 87.55824 start vw surface at 0.1500000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 166595 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22450 grid for indexing accessible points = 1.400000 m= 85343 mr = 116726 m= 33622 mr = 68414 m= 8922 mr = 26935 m= 1441 mr = 6556 m= 128 mr = 964 m= 3 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.7900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.360000 number of dielectric boundary points 76403 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 17184 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) : 1.954290 object centre at (A) : -3.497500 49.13400 13.76350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4718669 0.4949783 midg,1,midg; midg,igrid,midg -4.3168552E-02 0.2888651 1,midg,midg; igrid,midg,midg 0.8088039 0.2888434 gauss-seidel spectral radius is 0.9992812 estimated iterations to convergence 294 setup time was (sec) 1.690000 now iterating at: 22:46:01 rms-change max change #iterations 9.642320 420.6670 at 10iterations 5.745711 151.0057 at 20iterations 3.403620 79.40947 at 30iterations 2.004483 46.18244 at 40iterations 1.174973 29.06839 at 50iterations 0.6884237 15.54720 at 60iterations 0.4019268 8.396140 at 70iterations 0.2343334 4.748379 at 80iterations 0.1361731 2.665171 at 90iterations 7.9209648E-02 1.522321 at 100iterations 4.6087302E-02 0.8968122 at 110iterations 2.6803039E-02 0.5826101 at 120iterations 1.5552188E-02 0.2878914 at 130iterations 9.0339603E-03 0.1745548 at 140iterations 5.2477899E-03 0.1018125 at 150iterations 3.0463247E-03 6.2756538E-02 at 160iterations 1.7741059E-03 3.3607483E-02 at 170iterations 1.0358574E-03 1.8671036E-02 at 180iterations finished qdiffx linear iterations at : 22:46:13 total time elapsed so far: 13.46000 # loops : 180 mean,max change (kT/e) : 1.0358574E-03 1.8671036E-02 energy calculations done at 13.46000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.64000 DelPhi exited at 22:46:13 13.646u 0.295s 0:14.23 97.8% 0+0k 0+0io 0pf+0w