Sat Oct 15 10:25:44 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 10:25:44 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 = 2681 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: 0.5716396 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): -15.24600 40.47300 ymin,ymax (A): 28.84400 75.18000 zmin,zma (A): -10.33800 51.93900 x,y,z range (A): 55.71900 46.33600 62.27700 scale (grids/A): 0.5716396 object centre (A): 12.61350 52.01200 20.80050 number of atom coordinates read : 2681 total number of charged atoms : 2530 net assigned charge : -4.999990 assigned positive charge : 392.3934 centred at (gu) : 90.19294 91.24508 90.30769 assigned negative charge : -397.3943 centred at (gu) : 90.21596 91.23021 90.30179 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5720 nv = 96 ne = 84 npr = 53850 no. pairs analyzed = 53850 no. exposed pairs = 3496 no. arc points = 24833 no. surface atoms = 1182 nbur = 1499 mkacc time = 0.1400000 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 = 1.512000 m= 252 mr = 2916 m= 0 mr = 12 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3044 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2401 ## 266 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 7255 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.4088769E-10 -7.8055895E-10 midg,1,midg; midg,igrid,midg -7.7743201E-10 -7.8918933E-10 1,midg,midg; igrid,midg,midg -4.5457330E-10 -1.2109093E-09 gauss-seidel spectral radius is 0.9841883 estimated iterations to convergence 65 setup time was (sec) 0.5800000 now iterating at: 10:25:45 rms-change max change #iterations 8.7223530E-02 15.48402 at 10iterations 6.4259772E-03 1.009521 at 20iterations 4.7346656E-04 7.8128815E-02 at 30iterations 3.6631198E-05 6.3133240E-03 at 40iterations 2.9712342E-06 4.3487549E-04 at 50iterations finished qdiffx linear iterations at : 10:25:48 total time elapsed so far: 3.920000 # loops : 50 mean,max change (kT/e) : 2.9712342E-06 4.3487549E-04 energy calculations done at 3.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.090000 DelPhi exited at 10:25:49 4.091u 0.432s 0:05.22 86.5% 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 Sat Oct 15 2011 at 10:25:49 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 = 2681 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: 1.714919 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): -15.24600 40.47300 ymin,ymax (A): 28.84400 75.18000 zmin,zma (A): -10.33800 51.93900 x,y,z range (A): 55.71900 46.33600 62.27700 scale (grids/A): 1.714919 object centre (A): 12.61350 52.01200 20.80050 number of atom coordinates read : 2681 total number of charged atoms : 2530 net assigned charge : -4.999990 assigned positive charge : 392.3934 centred at (gu) : 90.57805 93.73470 90.92224 assigned negative charge : -397.3943 centred at (gu) : 90.64777 93.69041 90.90512 start vw surface at 0.1100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 62802 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24833 grid for indexing accessible points = 1.400000 m= 19702 mr = 41724 m= 2337 mr = 13703 m= 71 mr = 1251 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 28221 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 232 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 19565 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) : 0.5716396 object centre at (A) : 12.61350 52.01200 20.80050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.5269920E-03 -3.2985281E-02 midg,1,midg; midg,igrid,midg 5.1051396E-04 -4.4542346E-03 1,midg,midg; igrid,midg,midg -9.9990731E-03 -5.1207393E-03 gauss-seidel spectral radius is 0.9983289 estimated iterations to convergence 194 setup time was (sec) 0.8000000 now iterating at: 10:25:50 rms-change max change #iterations 3.447657 177.2938 at 10iterations 1.482356 70.36342 at 20iterations 0.6389499 22.54919 at 30iterations 0.2755962 10.75402 at 40iterations 0.1191847 4.522282 at 50iterations 5.1339686E-02 2.117871 at 60iterations 2.2190889E-02 0.7920561 at 70iterations 9.5480178E-03 0.3991833 at 80iterations 4.1503473E-03 0.1468925 at 90iterations 1.7885412E-03 6.6259384E-02 at 100iterations 7.7472907E-04 2.5238410E-02 at 110iterations 3.3313871E-04 1.1315346E-02 at 120iterations finished qdiffx linear iterations at : 10:25:59 total time elapsed so far: 9.330000 # loops : 120 mean,max change (kT/e) : 3.3313871E-04 1.1315346E-02 energy calculations done at 9.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.490000 DelPhi exited at 10:26:00 9.493u 0.481s 0:10.54 94.5% 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 10:26:00 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2681 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: 2.572378 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): -15.24600 40.47300 ymin,ymax (A): 28.84400 75.18000 zmin,zma (A): -10.33800 51.93900 x,y,z range (A): 55.71900 46.33600 62.27700 scale (grids/A): 2.572378 object centre (A): 12.61350 52.01200 20.80050 number of atom coordinates read : 2681 total number of charged atoms : 2530 net assigned charge : -4.999990 assigned positive charge : 392.3934 centred at (gu) : 90.86684 95.60178 91.38321 assigned negative charge : -397.3943 centred at (gu) : 90.97155 95.53551 91.35769 start vw surface at 0.1300000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 145936 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24833 grid for indexing accessible points = 1.400000 m= 66698 mr = 102390 m= 20380 mr = 52693 m= 3690 mr = 15571 m= 331 mr = 2477 m= 8 mr = 165 m= 0 mr = 2 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.250000 number of dielectric boundary points 63745 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 20231 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) : 1.714919 object centre at (A) : 12.61350 52.01200 20.80050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.8615835E-02 -0.4285751 midg,1,midg; midg,igrid,midg 1.9082358E-02 -9.1261409E-02 1,midg,midg; igrid,midg,midg -0.1178476 -2.8599469E-02 gauss-seidel spectral radius is 0.9991765 estimated iterations to convergence 275 setup time was (sec) 1.580000 now iterating at: 10:26:02 rms-change max change #iterations 8.742437 355.9784 at 10iterations 4.960883 141.3402 at 20iterations 2.800234 65.67906 at 30iterations 1.580207 37.48976 at 40iterations 0.8847833 21.72837 at 50iterations 0.4966621 10.53696 at 60iterations 0.2774285 6.373497 at 70iterations 0.1546239 3.600441 at 80iterations 8.6280532E-02 1.870747 at 90iterations 4.8178077E-02 1.034984 at 100iterations 2.6833903E-02 0.5711613 at 110iterations 1.4916277E-02 0.3559380 at 120iterations 8.3372984E-03 0.1807818 at 130iterations 4.6364260E-03 9.6854210E-02 at 140iterations 2.5807733E-03 5.2105188E-02 at 150iterations 1.4359632E-03 3.4391403E-02 at 160iterations 8.0110086E-04 1.7408371E-02 at 170iterations 4.4483837E-04 9.3498230E-03 at 180iterations finished qdiffx linear iterations at : 10:26:22 total time elapsed so far: 21.82000 # loops : 180 mean,max change (kT/e) : 4.4483837E-04 9.3498230E-03 energy calculations done at 21.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 22.00000 DelPhi exited at 10:26:23 22.002u 0.490s 0:23.33 96.3% 0+0k 0+0io 0pf+0w