Wed Feb 15 08:53:47 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:53:47 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: 212 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1874 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7011601 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): -19.30700 23.05100 ymin,ymax (A): -16.14100 24.38700 zmin,zma (A): 4.222000 54.99500 x,y,z range (A): 42.35800 40.52800 50.77300 scale (grids/A): 0.7011601 object centre (A): 1.872000 4.123000 29.60850 number of atom coordinates read : 1874 total number of charged atoms : 1743 net assigned charge : -0.9999905 assigned positive charge : 271.9783 centred at (gu) : 89.79371 88.48589 88.51944 assigned negative charge : -272.9782 centred at (gu) : 89.84771 88.62692 88.52699 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 6179 nv = 96 ne = 84 npr = 40372 no. pairs analyzed = 40372 no. exposed pairs = 2251 no. arc points = 16296 no. surface atoms = 747 nbur = 1127 mkacc time = 7.0000000E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 380 mr = 3457 m= 2 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 8.0000006E-02 no. cavity mid-points inaccessible to solvent = 168 time to turn everything in is 0.1500000 number of dielectric boundary points 3057 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1467 ## 118 charges are in solution ## iepsmp to db, and charging done at 0.2200000 number of grid points assigned charge 6872 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.0548682E-09 -8.2823153E-09 midg,1,midg; midg,igrid,midg 5.9803078E-08 -4.5696773E-08 1,midg,midg; igrid,midg,midg 1.2442755E-08 -2.7345457E-08 gauss-seidel spectral radius is 0.9893808 estimated iterations to convergence 79 setup time was (sec) 0.3400000 now iterating at: 08:53:48 rms-change max change #iterations 0.1812046 26.03537 at 10iterations 2.1649981E-02 3.503760 at 20iterations 2.6212544E-03 0.3870342 at 30iterations 3.1809401E-04 4.5799255E-02 at 40iterations 3.8000919E-05 6.0005188E-03 at 50iterations finished qdiffx linear iterations at : 08:53:50 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 3.8000919E-05 6.0005188E-03 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 08:53:51 3.332u 0.179s 0:04.14 84.5% 0+0k 0+0io 6pf+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 Wed Feb 15 2012 at 08:53:51 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: 212 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1874 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.103480 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): -19.30700 23.05100 ymin,ymax (A): -16.14100 24.38700 zmin,zma (A): 4.222000 54.99500 x,y,z range (A): 42.35800 40.52800 50.77300 scale (grids/A): 2.103480 object centre (A): 1.872000 4.123000 29.60850 number of atom coordinates read : 1874 total number of charged atoms : 1743 net assigned charge : -0.9999905 assigned positive charge : 271.9783 centred at (gu) : 89.38130 85.45769 85.55848 assigned negative charge : -272.9782 centred at (gu) : 89.54327 85.88081 85.58103 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 65415 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16296 grid for indexing accessible points = 1.400000 m= 24914 mr = 45566 m= 4742 mr = 18522 m= 477 mr = 3112 m= 14 mr = 194 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 4328 time to turn everything in is 0.3200000 number of dielectric boundary points 28168 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 67 iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 13831 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) : 0.7011601 object centre at (A) : 1.872000 4.123000 29.60850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8334916E-02 -1.8784754E-02 midg,1,midg; midg,igrid,midg 2.8225881E-04 -9.0203658E-03 1,midg,midg; igrid,midg,midg 1.3678052E-02 -4.5120423E-03 gauss-seidel spectral radius is 0.9987941 estimated iterations to convergence 228 setup time was (sec) 0.5300000 now iterating at: 08:53:52 rms-change max change #iterations 4.234154 230.7628 at 10iterations 2.061956 79.80287 at 20iterations 1.009938 36.52147 at 30iterations 0.4962686 16.01532 at 40iterations 0.2431230 8.024043 at 50iterations 0.1190602 4.118034 at 60iterations 5.8143053E-02 1.846912 at 70iterations 2.8519774E-02 0.8710632 at 80iterations 1.4039955E-02 0.4859290 at 90iterations 6.8591232E-03 0.2107239 at 100iterations 3.3683463E-03 0.1039772 at 110iterations 1.6468861E-03 5.0155640E-02 at 120iterations finished qdiffx linear iterations at : 08:53:59 total time elapsed so far: 7.580000 # loops : 120 mean,max change (kT/e) : 1.6468861E-03 5.0155640E-02 energy calculations done at 7.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 08:54:00 7.718u 0.199s 0:08.31 95.0% 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 Wed Feb 15 2012 at 08:54:00 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: 212 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1874 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.155220 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): -19.30700 23.05100 ymin,ymax (A): -16.14100 24.38700 zmin,zma (A): 4.222000 54.99500 x,y,z range (A): 42.35800 40.52800 50.77300 scale (grids/A): 3.155220 object centre (A): 1.872000 4.123000 29.60850 number of atom coordinates read : 1874 total number of charged atoms : 1743 net assigned charge : -0.9999905 assigned positive charge : 271.9783 centred at (gu) : 89.07188 83.18667 83.33781 assigned negative charge : -272.9782 centred at (gu) : 89.31489 83.82126 83.37157 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 151129 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16296 grid for indexing accessible points = 1.400000 m= 77854 mr = 110007 m= 30791 mr = 64114 m= 8923 mr = 24930 m= 1843 mr = 6875 m= 180 mr = 1256 m= 6 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 15169 time to turn everything in is 1.000000 number of dielectric boundary points 63472 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 13944 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) : 2.103480 object centre at (A) : 1.872000 4.123000 29.60850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2422013 -0.1251644 midg,1,midg; midg,igrid,midg -8.7502450E-03 -0.1164805 1,midg,midg; igrid,midg,midg 0.1042400 -2.2497075E-02 gauss-seidel spectral radius is 0.9992799 estimated iterations to convergence 294 setup time was (sec) 1.240000 now iterating at: 08:54:01 rms-change max change #iterations 9.369821 470.1318 at 10iterations 5.398167 122.4569 at 20iterations 3.124001 71.69354 at 30iterations 1.807481 36.37857 at 40iterations 1.043422 19.12982 at 50iterations 0.6039662 11.03146 at 60iterations 0.3491523 6.738145 at 70iterations 0.2019995 3.990982 at 80iterations 0.1163430 2.310394 at 90iterations 6.7346089E-02 1.412483 at 100iterations 3.8862441E-02 0.7637091 at 110iterations 2.2495111E-02 0.4189988 at 120iterations 1.3029897E-02 0.2491350 at 130iterations 7.5096488E-03 0.1311817 at 140iterations 4.3418333E-03 8.5415363E-02 at 150iterations 2.5080426E-03 4.8305511E-02 at 160iterations 1.4507100E-03 2.7165413E-02 at 170iterations 8.3894795E-04 1.5111923E-02 at 180iterations finished qdiffx linear iterations at : 08:54:13 total time elapsed so far: 12.81000 # loops : 180 mean,max change (kT/e) : 8.3894795E-04 1.5111923E-02 energy calculations done at 12.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.94000 DelPhi exited at 08:54:13 12.946u 0.202s 0:13.54 97.0% 0+0k 0+0io 0pf+0w