Wed Feb 15 08:54:32 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 08:54:32 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2364 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6704963 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): -21.78100 31.31400 ymin,ymax (A): 12.10400 57.99800 zmin,zma (A): 27.96100 78.26200 x,y,z range (A): 53.09500 45.89400 50.30100 scale (grids/A): 0.6704963 object centre (A): 4.766500 35.05100 53.11150 number of atom coordinates read : 2364 total number of charged atoms : 2231 net assigned charge : -3.499990 assigned positive charge : 358.1852 centred at (gu) : 89.38589 90.68959 90.31360 assigned negative charge : -361.6858 centred at (gu) : 89.56557 90.68001 90.39175 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7154 nv = 96 ne = 84 npr = 49851 no. pairs analyzed = 49851 no. exposed pairs = 2905 no. arc points = 20591 no. surface atoms = 986 nbur = 1378 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 447 mr = 3988 m= 1 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 54 time to turn everything in is 0.1900000 number of dielectric boundary points 3537 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1918 ## 144 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8396 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.1973986E-09 -3.2944332E-08 midg,1,midg; midg,igrid,midg -1.2436631E-08 -1.1058043E-08 1,midg,midg; igrid,midg,midg 3.4682635E-08 -4.9287021E-08 gauss-seidel spectral radius is 0.9884489 estimated iterations to convergence 76 setup time was (sec) 0.4300000 now iterating at: 08:54:33 rms-change max change #iterations 0.1704270 24.32981 at 10iterations 1.9249091E-02 2.717598 at 20iterations 2.1362554E-03 0.2838173 at 30iterations 2.5071102E-04 3.5019875E-02 at 40iterations 3.7891714E-05 7.3766708E-03 at 50iterations finished qdiffx linear iterations at : 08:54:36 total time elapsed so far: 3.730000 # loops : 50 mean,max change (kT/e) : 3.7891714E-05 7.3766708E-03 energy calculations done at 3.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.850000 DelPhi exited at 08:54:37 3.853u 0.254s 0:04.68 87.6% 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 Wed Feb 15 2012 at 08:54:37 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2364 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.011489 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): -21.78100 31.31400 ymin,ymax (A): 12.10400 57.99800 zmin,zma (A): 27.96100 78.26200 x,y,z range (A): 53.09500 45.89400 50.30100 scale (grids/A): 2.011489 object centre (A): 4.766500 35.05100 53.11150 number of atom coordinates read : 2364 total number of charged atoms : 2231 net assigned charge : -3.499990 assigned positive charge : 358.1852 centred at (gu) : 88.15723 92.06847 90.94037 assigned negative charge : -361.6858 centred at (gu) : 88.69660 92.03989 91.17509 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 76369 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20591 grid for indexing accessible points = 1.400000 m= 28791 mr = 53078 m= 5365 mr = 21438 m= 456 mr = 3597 m= 8 mr = 222 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 1921 time to turn everything in is 0.4100000 number of dielectric boundary points 32654 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 109 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 17655 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) : 0.6704963 object centre at (A) : 4.766500 35.05100 53.11150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8625487E-02 -4.3342251E-02 midg,1,midg; midg,igrid,midg -1.1288851E-02 -4.2983948E-04 1,midg,midg; igrid,midg,midg 3.1449299E-02 -6.5926169E-03 gauss-seidel spectral radius is 0.9987494 estimated iterations to convergence 224 setup time was (sec) 0.6700000 now iterating at: 08:54:38 rms-change max change #iterations 4.534381 201.1669 at 10iterations 2.190880 70.89680 at 20iterations 1.053419 32.50893 at 30iterations 0.5106463 15.60498 at 40iterations 0.2469537 7.387341 at 50iterations 0.1192367 3.357036 at 60iterations 5.7605546E-02 1.748402 at 70iterations 2.7902208E-02 0.9059811 at 80iterations 1.3520063E-02 0.4081223 at 90iterations 6.5384996E-03 0.1945724 at 100iterations 3.1820959E-03 0.1008377 at 110iterations 1.5427402E-03 4.5375824E-02 at 120iterations finished qdiffx linear iterations at : 08:54:46 total time elapsed so far: 8.460000 # loops : 120 mean,max change (kT/e) : 1.5427402E-03 4.5375824E-02 energy calculations done at 8.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.590000 DelPhi exited at 08:54:47 8.595u 0.293s 0:09.51 93.3% 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 08:54:47 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: 280 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2364 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.017233 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): -21.78100 31.31400 ymin,ymax (A): 12.10400 57.99800 zmin,zma (A): 27.96100 78.26200 x,y,z range (A): 53.09500 45.89400 50.30100 scale (grids/A): 3.017233 object centre (A): 4.766500 35.05100 53.11150 number of atom coordinates read : 2364 total number of charged atoms : 2231 net assigned charge : -3.499990 assigned positive charge : 358.1852 centred at (gu) : 87.23571 93.10246 91.41053 assigned negative charge : -361.6858 centred at (gu) : 88.04491 93.05995 91.76262 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 176439 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20591 grid for indexing accessible points = 1.400000 m= 90595 mr = 128222 m= 35689 mr = 74556 m= 10175 mr = 29157 m= 1973 mr = 7951 m= 187 mr = 1438 m= 5 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 6213 time to turn everything in is 1.090000 number of dielectric boundary points 73644 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 17848 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) : 2.011489 object centre at (A) : 4.766500 35.05100 53.11150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4250014 -0.2401628 midg,1,midg; midg,igrid,midg -3.4741376E-02 0.1319832 1,midg,midg; igrid,midg,midg 0.3294301 1.1663593E-02 gauss-seidel spectral radius is 0.9992827 estimated iterations to convergence 295 setup time was (sec) 1.380000 now iterating at: 08:54:49 rms-change max change #iterations 10.41839 336.4521 at 10iterations 6.129021 148.3233 at 20iterations 3.594727 70.48920 at 30iterations 2.102602 47.03996 at 40iterations 1.224523 24.27905 at 50iterations 0.7152237 12.95547 at 60iterations 0.4171791 7.972188 at 70iterations 0.2425976 5.288208 at 80iterations 0.1406951 2.697521 at 90iterations 8.1871845E-02 1.460547 at 100iterations 4.7559962E-02 0.8026257 at 110iterations 2.7689405E-02 0.5555849 at 120iterations 1.6068311E-02 0.3063660 at 130iterations 9.3390830E-03 0.1522732 at 140iterations 5.4489924E-03 9.6231461E-02 at 150iterations 3.1852380E-03 5.5009842E-02 at 160iterations 1.8728335E-03 3.3990860E-02 at 170iterations 1.1172752E-03 2.1634579E-02 at 180iterations finished qdiffx linear iterations at : 08:55:02 total time elapsed so far: 14.21000 # loops : 180 mean,max change (kT/e) : 1.1172752E-03 2.1634579E-02 energy calculations done at 14.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.35000 DelPhi exited at 08:55:03 14.349u 0.383s 0:15.23 96.6% 0+0k 0+0io 0pf+0w