Wed Feb 15 08:55:36 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 08:55:36 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 = 2393 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: 0.6068975 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): 39.95900 98.61800 ymin,ymax (A): -5.010000 48.01700 zmin,zma (A): -0.8390000 43.81400 x,y,z range (A): 58.65900 53.02700 44.65300 scale (grids/A): 0.6068975 object centre (A): 69.28850 21.50350 21.48750 number of atom coordinates read : 2393 total number of charged atoms : 2256 net assigned charge : 1.000008 assigned positive charge : 364.2832 centred at (gu) : 90.43710 89.81086 90.84017 assigned negative charge : -363.2836 centred at (gu) : 90.58119 89.88485 90.65811 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5862 nv = 96 ne = 84 npr = 48607 no. pairs analyzed = 48607 no. exposed pairs = 3264 no. arc points = 22452 no. surface atoms = 1103 nbur = 1290 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 231 mr = 2900 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3184 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2323 ## 249 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7321 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.0587886E-09 9.7249240E-09 midg,1,midg; midg,igrid,midg 3.7523797E-09 -2.5353197E-09 1,midg,midg; igrid,midg,midg 5.8666094E-09 -6.2845071E-09 gauss-seidel spectral radius is 0.9859306 estimated iterations to convergence 69 setup time was (sec) 0.5300000 now iterating at: 08:55:37 rms-change max change #iterations 0.1066352 18.27087 at 10iterations 9.3449540E-03 1.435570 at 20iterations 8.2863250E-04 0.1410561 at 30iterations 9.8074015E-05 1.6886711E-02 at 40iterations 2.5377842E-05 5.8813095E-03 at 50iterations finished qdiffx linear iterations at : 08:55:40 total time elapsed so far: 3.580000 # loops : 50 mean,max change (kT/e) : 2.5377842E-05 5.8813095E-03 energy calculations done at 3.580000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.770000 DelPhi exited at 08:55:41 3.770u 0.235s 0:04.48 89.2% 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 08:55:41 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 = 2393 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: 1.820692 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): 39.95900 98.61800 ymin,ymax (A): -5.010000 48.01700 zmin,zma (A): -0.8390000 43.81400 x,y,z range (A): 58.65900 53.02700 44.65300 scale (grids/A): 1.820692 object centre (A): 69.28850 21.50350 21.48750 number of atom coordinates read : 2393 total number of charged atoms : 2256 net assigned charge : 1.000008 assigned positive charge : 364.2832 centred at (gu) : 91.31074 89.43192 92.51994 assigned negative charge : -363.2836 centred at (gu) : 91.74339 89.65432 91.97404 start vw surface at 0.1700000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 63669 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22452 grid for indexing accessible points = 1.400000 m= 19900 mr = 42017 m= 2195 mr = 13401 m= 97 mr = 1049 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 29388 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 188 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 17649 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) : 0.6068975 object centre at (A) : 69.28850 21.50350 21.48750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1588222E-03 1.9726699E-02 midg,1,midg; midg,igrid,midg 3.1430977E-03 -2.0614702E-02 1,midg,midg; igrid,midg,midg 2.7325016E-02 -4.3906845E-02 gauss-seidel spectral radius is 0.9984885 estimated iterations to convergence 204 setup time was (sec) 0.8200000 now iterating at: 08:55:42 rms-change max change #iterations 3.723600 196.1583 at 10iterations 1.658741 60.80813 at 20iterations 0.7455931 29.98346 at 30iterations 0.3329343 11.14298 at 40iterations 0.1494073 5.259090 at 50iterations 6.7502148E-02 2.342804 at 60iterations 3.0277226E-02 1.082350 at 70iterations 1.3589614E-02 0.4676552 at 80iterations 6.1204638E-03 0.2098370 at 90iterations 2.7531455E-03 9.9687576E-02 at 100iterations 1.2406500E-03 4.4291973E-02 at 110iterations 5.6543760E-04 2.1033764E-02 at 120iterations finished qdiffx linear iterations at : 08:55:49 total time elapsed so far: 7.760000 # loops : 120 mean,max change (kT/e) : 5.6543760E-04 2.1033764E-02 energy calculations done at 7.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.950000 DelPhi exited at 08:55:50 7.950u 0.367s 0:09.05 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 Wed Feb 15 2012 at 08:55:50 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 = 2393 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.731039 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): 39.95900 98.61800 ymin,ymax (A): -5.010000 48.01700 zmin,zma (A): -0.8390000 43.81400 x,y,z range (A): 58.65900 53.02700 44.65300 scale (grids/A): 2.731039 object centre (A): 69.28850 21.50350 21.48750 number of atom coordinates read : 2393 total number of charged atoms : 2256 net assigned charge : 1.000008 assigned positive charge : 364.2832 centred at (gu) : 91.96589 89.14767 93.77969 assigned negative charge : -363.2836 centred at (gu) : 92.61504 89.48143 92.96098 start vw surface at 0.1500000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 147571 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22452 grid for indexing accessible points = 1.400000 m= 68143 mr = 103183 m= 19767 mr = 53065 m= 3494 mr = 14535 m= 380 mr = 2226 m= 20 mr = 190 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.180000 number of dielectric boundary points 66176 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 18045 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) : 1.820692 object centre at (A) : 69.28850 21.50350 21.48750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3476271E-03 0.1699203 midg,1,midg; midg,igrid,midg 0.1172339 -0.3298675 1,midg,midg; igrid,midg,midg 0.3587654 -0.6768096 gauss-seidel spectral radius is 0.9992235 estimated iterations to convergence 283 setup time was (sec) 1.510000 now iterating at: 08:55:52 rms-change max change #iterations 9.070865 257.9886 at 10iterations 5.281813 155.6689 at 20iterations 3.048119 64.70105 at 30iterations 1.745072 36.53774 at 40iterations 0.9993439 23.04078 at 50iterations 0.5708674 12.21323 at 60iterations 0.3256053 6.438835 at 70iterations 0.1854475 4.242968 at 80iterations 0.1055393 2.172098 at 90iterations 5.9857268E-02 1.246433 at 100iterations 3.4009423E-02 0.6626902 at 110iterations 1.9296871E-02 0.3906708 at 120iterations 1.0949854E-02 0.2302375 at 130iterations 6.2094708E-03 0.1471150 at 140iterations 3.5163141E-03 7.5573444E-02 at 150iterations 1.9970383E-03 3.7714958E-02 at 160iterations 1.1303989E-03 2.2888184E-02 at 170iterations 6.4108503E-04 1.2957573E-02 at 180iterations finished qdiffx linear iterations at : 08:56:03 total time elapsed so far: 12.80000 # loops : 180 mean,max change (kT/e) : 6.4108503E-04 1.2957573E-02 energy calculations done at 12.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.00000 DelPhi exited at 08:56:06 12.999u 0.292s 0:16.02 82.8% 0+0k 0+0io 0pf+0w