Sat Oct 15 11:29:37 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 15 2011 at 11:29:37 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 = 3519 !!! WARNING: ILE 447 has a net charge of -0.2720 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: 0.5255466 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): 0.1830000 44.62200 ymin,ymax (A): -30.48300 25.99600 zmin,zma (A): 1.641000 69.38000 x,y,z range (A): 44.43900 56.47900 67.73901 scale (grids/A): 0.5255466 object centre (A): 22.40250 -2.243500 35.51050 number of atom coordinates read : 3519 total number of charged atoms : 3372 net assigned charge : -5.771984 assigned positive charge : 533.0622 centred at (gu) : 90.24857 91.68146 90.49126 assigned negative charge : -538.8358 centred at (gu) : 90.19611 91.64297 90.49094 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6090 nv = 96 ne = 84 npr = 71834 no. pairs analyzed = 71834 no. exposed pairs = 4227 no. arc points = 28985 no. surface atoms = 1435 nbur = 2084 mkacc time = 0.1200000 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 = 1.624000 m= 249 mr = 3258 m= 0 mr = 8 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3073 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2957 ## 437 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 8221 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4199089E-10 -1.7874938E-10 midg,1,midg; midg,igrid,midg -1.9613249E-10 -2.6754203E-11 1,midg,midg; igrid,midg,midg -3.2939310E-10 3.2309953E-11 gauss-seidel spectral radius is 0.9813817 estimated iterations to convergence 60 setup time was (sec) 0.4800000 now iterating at: 11:29:38 rms-change max change #iterations 6.6728614E-02 10.07437 at 10iterations 4.1204155E-03 0.5849686 at 20iterations 3.6579726E-04 6.2379837E-02 at 30iterations 7.0853988E-05 1.4763832E-02 at 40iterations 1.7258608E-05 3.6573410E-03 at 50iterations finished qdiffx linear iterations at : 11:29:41 total time elapsed so far: 3.780000 # loops : 50 mean,max change (kT/e) : 1.7258608E-05 3.6573410E-03 energy calculations done at 3.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.910000 DelPhi exited at 11:29:42 3.909u 0.235s 0:04.69 88.0% 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 Sat Oct 15 2011 at 11:29:42 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 = 3519 !!! WARNING: ILE 447 has a net charge of -0.2720 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: 1.576640 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): 0.1830000 44.62200 ymin,ymax (A): -30.48300 25.99600 zmin,zma (A): 1.641000 69.38000 x,y,z range (A): 44.43900 56.47900 67.73901 scale (grids/A): 1.576640 object centre (A): 22.40250 -2.243500 35.51050 number of atom coordinates read : 3519 total number of charged atoms : 3372 net assigned charge : -5.771984 assigned positive charge : 533.0622 centred at (gu) : 90.74490 95.04319 91.47276 assigned negative charge : -538.8358 centred at (gu) : 90.58797 94.92859 91.47240 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 69411 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28985 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 21023 mr = 48550 m= 1848 mr = 14517 m= 38 mr = 845 m= 0 mr = 2 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 419 time to turn everything in is 0.3400000 number of dielectric boundary points 28406 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 376 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 25565 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) : 0.5255466 object centre at (A) : 22.40250 -2.243500 35.51050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.6349089E-03 1.1435962E-02 midg,1,midg; midg,igrid,midg -8.2049370E-03 -1.1000821E-02 1,midg,midg; igrid,midg,midg -5.0261831E-03 8.4734935E-04 gauss-seidel spectral radius is 0.9980886 estimated iterations to convergence 182 setup time was (sec) 0.5500000 now iterating at: 11:29:43 rms-change max change #iterations 3.408855 151.8703 at 10iterations 1.388194 54.92419 at 20iterations 0.5661790 19.10738 at 30iterations 0.2314079 7.737432 at 40iterations 9.4544113E-02 3.285275 at 50iterations 3.8579848E-02 1.433754 at 60iterations 1.5761433E-02 0.5423212 at 70iterations 6.4863157E-03 0.2167935 at 80iterations 2.6629018E-03 9.1384888E-02 at 90iterations 1.1180483E-03 4.4227600E-02 at 100iterations 4.8113608E-04 1.7663956E-02 at 110iterations 2.1760465E-04 8.6853504E-03 at 120iterations finished qdiffx linear iterations at : 11:29:52 total time elapsed so far: 7.620000 # loops : 120 mean,max change (kT/e) : 2.1760465E-04 8.6853504E-03 energy calculations done at 7.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 11:29:53 7.748u 0.215s 0:11.02 72.1% 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 15 2011 at 11:29:53 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 = 3519 !!! WARNING: ILE 447 has a net charge of -0.2720 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: 2.364959 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): 0.1830000 44.62200 ymin,ymax (A): -30.48300 25.99600 zmin,zma (A): 1.641000 69.38000 x,y,z range (A): 44.43900 56.47900 67.73901 scale (grids/A): 2.364959 object centre (A): 22.40250 -2.243500 35.51050 number of atom coordinates read : 3519 total number of charged atoms : 3372 net assigned charge : -5.771984 assigned positive charge : 533.0622 centred at (gu) : 91.11709 97.56458 92.20890 assigned negative charge : -538.8358 centred at (gu) : 90.88196 97.39277 92.20850 start vw surface at 0.1100000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 161646 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28985 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 74502 mr = 118943 m= 19615 mr = 59050 m= 2876 mr = 14699 m= 163 mr = 1905 m= 1 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 1442 time to turn everything in is 0.8200000 number of dielectric boundary points 64151 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 34 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 26937 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) : 1.576640 object centre at (A) : 22.40250 -2.243500 35.51050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2760684 9.3560293E-02 midg,1,midg; midg,igrid,midg -0.1134733 -0.1434657 1,midg,midg; igrid,midg,midg -8.3412483E-02 2.8655948E-02 gauss-seidel spectral radius is 0.9991137 estimated iterations to convergence 265 setup time was (sec) 1.060000 now iterating at: 11:29:54 rms-change max change #iterations 8.920993 259.6619 at 10iterations 4.952959 113.8396 at 20iterations 2.736818 85.68919 at 30iterations 1.502052 30.64454 at 40iterations 0.8254849 17.62518 at 50iterations 0.4511901 10.87046 at 60iterations 0.2471892 4.960450 at 70iterations 0.1349123 2.685707 at 80iterations 7.3733322E-02 1.517847 at 90iterations 4.0213626E-02 0.7811317 at 100iterations 2.1937801E-02 0.4650939 at 110iterations 1.1989857E-02 0.2497005 at 120iterations 6.5361946E-03 0.1422272 at 130iterations 3.5642830E-03 7.5715065E-02 at 140iterations 1.9528770E-03 3.8032532E-02 at 150iterations 1.0694650E-03 2.2178650E-02 at 160iterations 5.8807287E-04 1.3270378E-02 at 170iterations 3.2779202E-04 6.6375732E-03 at 180iterations finished qdiffx linear iterations at : 11:30:16 total time elapsed so far: 12.26000 # loops : 180 mean,max change (kT/e) : 3.2779202E-04 6.6375732E-03 energy calculations done at 12.26000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.39000 DelPhi exited at 11:30:17 12.391u 0.206s 0:24.00 52.4% 0+0k 0+0io 0pf+0w