Mon Oct 10 14:00:35 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 Mon Oct 10 2011 at 14:00:35 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5052 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5640140 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): 3.227000 64.28800 ymin,ymax (A): -8.747000 54.37200 zmin,zma (A): -1.144000 61.48400 x,y,z range (A): 61.06100 63.11900 62.62800 scale (grids/A): 0.5640140 object centre (A): 33.75750 22.81250 30.17000 number of atom coordinates read : 5052 total number of charged atoms : 4905 net assigned charge : -1.878945 assigned positive charge : 774.8336 centred at (gu) : 88.38245 89.01806 89.21593 assigned negative charge : -776.7185 centred at (gu) : 88.27904 89.04063 89.18018 start vw surface at 0.2200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 10438 nv = 96 ne = 84 npr = 103034 no. pairs analyzed = 103034 no. exposed pairs = 5878 no. arc points = 39800 no. surface atoms = 2000 nbur = 3052 mkacc time = 0.2400000 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 = 1.540000 m= 488 mr = 6033 m= 3 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 4875 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4102 ## 426 charges are in solution ## iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 13793 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1900082E-09 4.9660975E-10 midg,1,midg; midg,igrid,midg 4.0170045E-10 -5.4484506E-10 1,midg,midg; igrid,midg,midg -3.7380157E-09 1.4028125E-09 gauss-seidel spectral radius is 0.9839344 estimated iterations to convergence 65 setup time was (sec) 0.7500000 now iterating at: 14:00:36 rms-change max change #iterations 0.1207126 15.37635 at 10iterations 1.1548397E-02 1.624626 at 20iterations 3.2228590E-03 0.3529205 at 30iterations 1.4036200E-03 0.1637101 at 40iterations 6.3557382E-04 7.9515457E-02 at 50iterations finished qdiffx linear iterations at : 14:00:39 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 6.3557382E-04 7.9515457E-02 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.620000 DelPhi exited at 14:00:39 3.621u 0.164s 0:04.17 90.6% 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 14:00:40 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5052 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.692042 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): 3.227000 64.28800 ymin,ymax (A): -8.747000 54.37200 zmin,zma (A): -1.144000 61.48400 x,y,z range (A): 61.06100 63.11900 62.62800 scale (grids/A): 1.692042 object centre (A): 33.75750 22.81250 30.17000 number of atom coordinates read : 5052 total number of charged atoms : 4905 net assigned charge : -1.878945 assigned positive charge : 774.8336 centred at (gu) : 85.14601 87.05298 87.64627 assigned negative charge : -776.7185 centred at (gu) : 84.83709 87.12177 87.54039 start vw surface at 0.2400000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 116943 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39800 grid for indexing accessible points = 1.400000 m= 40980 mr = 85196 m= 5140 mr = 29828 m= 200 mr = 2842 m= 3 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 268 time to turn everything in is 0.9000000 number of dielectric boundary points 45372 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 374 ## 1 charges are in solution ## iepsmp to db, and charging done at 1.050000 number of grid points assigned charge 37803 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) : 0.5640140 object centre at (A) : 33.75750 22.81250 30.17000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1142443E-02 -2.8186180E-02 midg,1,midg; midg,igrid,midg 1.9319745E-02 8.0106454E-03 1,midg,midg; igrid,midg,midg -2.5243334E-02 1.7607493E-02 gauss-seidel spectral radius is 0.9984983 estimated iterations to convergence 205 setup time was (sec) 1.230000 now iterating at: 14:00:41 rms-change max change #iterations 5.034062 168.8573 at 10iterations 2.256996 66.85681 at 20iterations 1.021842 29.24702 at 30iterations 0.4629310 11.78901 at 40iterations 0.2099401 5.878062 at 50iterations 9.5452935E-02 2.439537 at 60iterations 4.3667946E-02 1.271667 at 70iterations 2.0279579E-02 0.5707321 at 80iterations 9.8267570E-03 0.2630615 at 90iterations 5.1503512E-03 0.1341057 at 100iterations 3.0181746E-03 8.4736824E-02 at 110iterations 1.9843183E-03 6.0043335E-02 at 120iterations finished qdiffx linear iterations at : 14:00:48 total time elapsed so far: 8.560000 # loops : 120 mean,max change (kT/e) : 1.9843183E-03 6.0043335E-02 energy calculations done at 8.560000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.780000 DelPhi exited at 14:00:49 8.786u 0.241s 0:09.73 92.7% 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 14:00:50 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5052 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.538063 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): 3.227000 64.28800 ymin,ymax (A): -8.747000 54.37200 zmin,zma (A): -1.144000 61.48400 x,y,z range (A): 61.06100 63.11900 62.62800 scale (grids/A): 2.538063 object centre (A): 33.75750 22.81250 30.17000 number of atom coordinates read : 5052 total number of charged atoms : 4905 net assigned charge : -1.878945 assigned positive charge : 774.8336 centred at (gu) : 82.71847 85.57905 86.46896 assigned negative charge : -776.7185 centred at (gu) : 82.25568 85.68272 86.31059 start vw surface at 0.2200000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 271732 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39800 grid for indexing accessible points = 1.400000 m= 137385 mr = 206778 m= 44688 mr = 112491 m= 8706 mr = 35104 m= 815 mr = 6153 m= 15 mr = 450 m= 0 mr = 4 time to grow re-entrant surface = 1.280000 no. cavity mid-points inaccessible to solvent = 902 time to turn everything in is 2.120000 number of dielectric boundary points 102361 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 21 iepsmp to db, and charging done at 2.290000 number of grid points assigned charge 39212 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) : 1.692042 object centre at (A) : 33.75750 22.81250 30.17000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4941543 -0.6862603 midg,1,midg; midg,igrid,midg 5.7188999E-03 4.6078581E-03 1,midg,midg; igrid,midg,midg -0.4021609 0.1944930 gauss-seidel spectral radius is 0.9992712 estimated iterations to convergence 292 setup time was (sec) 2.480000 now iterating at: 14:00:52 rms-change max change #iterations 12.54844 307.3652 at 10iterations 7.443760 151.2543 at 20iterations 4.376318 100.3923 at 30iterations 2.570052 45.42186 at 40iterations 1.503713 26.01745 at 50iterations 0.8771069 15.27241 at 60iterations 0.5105992 8.483191 at 70iterations 0.2968493 4.854609 at 80iterations 0.1723210 3.040945 at 90iterations 0.1002014 1.595495 at 100iterations 5.8202658E-02 0.9376183 at 110iterations 3.3929903E-02 0.5283334 at 120iterations 1.9934576E-02 0.3106499 at 130iterations 1.1880807E-02 0.1962366 at 140iterations 7.2763958E-03 0.1233692 at 150iterations 4.6589514E-03 8.3892822E-02 at 160iterations 3.1648856E-03 5.4971695E-02 at 170iterations 2.2995416E-03 3.7652493E-02 at 180iterations finished qdiffx linear iterations at : 14:01:04 total time elapsed so far: 14.20000 # loops : 180 mean,max change (kT/e) : 2.2995416E-03 3.7652493E-02 energy calculations done at 14.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.42000 DelPhi exited at 14:01:05 14.419u 0.219s 0:15.38 95.0% 0+0k 0+0io 0pf+0w