Sun Oct 9 08:56:15 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 Sun Oct 9 2011 at 08:56:15 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 = 5497 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5009568 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): 3.845000 74.90900 ymin,ymax (A): 22.52600 84.18800 zmin,zma (A): 6.300000 70.56900 x,y,z range (A): 71.06400 61.66199 64.26900 scale (grids/A): 0.5009568 object centre (A): 39.37700 53.35700 38.43450 number of atom coordinates read : 5497 total number of charged atoms : 5332 net assigned charge : -0.4999574 assigned positive charge : 825.9871 centred at (gu) : 90.06483 88.60967 89.13484 assigned negative charge : -826.4937 centred at (gu) : 89.89307 88.60723 89.03857 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8759 nv = 96 ne = 84 npr = 110036 no. pairs analyzed = 110036 no. exposed pairs = 6960 no. arc points = 48321 no. surface atoms = 2323 nbur = 3174 mkacc time = 0.1900000 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 = 1.708000 m= 274 mr = 4478 m= 0 mr = 5 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 4 time to turn everything in is 0.3400000 number of dielectric boundary points 4550 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4750 ## 773 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 11796 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4621941E-10 1.4575922E-10 midg,1,midg; midg,igrid,midg -1.0625532E-11 1.5087583E-12 1,midg,midg; igrid,midg,midg -3.4211550E-10 3.3318626E-10 gauss-seidel spectral radius is 0.9796779 estimated iterations to convergence 58 setup time was (sec) 0.5300000 now iterating at: 08:56:16 rms-change max change #iterations 6.5443076E-02 9.379193 at 10iterations 3.6631480E-03 0.5262604 at 20iterations 3.7346996E-04 8.9755535E-02 at 30iterations 9.5731157E-05 2.3139954E-02 at 40iterations 2.8749701E-05 6.6432953E-03 at 50iterations finished qdiffx linear iterations at : 08:56:19 total time elapsed so far: 3.400000 # loops : 50 mean,max change (kT/e) : 2.8749701E-05 6.6432953E-03 energy calculations done at 3.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 08:56:19 3.541u 0.171s 0:04.03 92.0% 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 Sun Oct 9 2011 at 08:56:19 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 = 5497 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.502871 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): 3.845000 74.90900 ymin,ymax (A): 22.52600 84.18800 zmin,zma (A): 6.300000 70.56900 x,y,z range (A): 71.06400 61.66199 64.26900 scale (grids/A): 1.502871 object centre (A): 39.37700 53.35700 38.43450 number of atom coordinates read : 5497 total number of charged atoms : 5332 net assigned charge : -0.4999574 assigned positive charge : 825.9871 centred at (gu) : 90.19258 85.82717 87.40252 assigned negative charge : -826.4937 centred at (gu) : 89.67888 85.82154 87.11527 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 99084 reading accessible surface arcs data from file ARCDAT no. of arc points read = 48321 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 26868 mr = 67634 m= 2018 mr = 17185 m= 31 mr = 783 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 2113 time to turn everything in is 0.4700000 number of dielectric boundary points 42400 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 750 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 39830 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) : 0.5009568 object centre at (A) : 39.37700 53.35700 38.43450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.4461963E-03 1.0667934E-02 midg,1,midg; midg,igrid,midg -3.0488332E-03 -5.4645482E-03 1,midg,midg; igrid,midg,midg -9.4866268E-03 3.2455474E-02 gauss-seidel spectral radius is 0.9980989 estimated iterations to convergence 182 setup time was (sec) 0.6800000 now iterating at: 08:56:20 rms-change max change #iterations 3.921895 144.2905 at 10iterations 1.604647 52.71822 at 20iterations 0.6554291 21.47193 at 30iterations 0.2684016 9.498381 at 40iterations 0.1095684 3.421833 at 50iterations 4.4700872E-02 1.350351 at 60iterations 1.8349649E-02 0.5955811 at 70iterations 7.5348187E-03 0.2338896 at 80iterations 3.1055177E-03 8.7709427E-02 at 90iterations 1.2813868E-03 4.3338776E-02 at 100iterations 5.3720345E-04 1.6795635E-02 at 110iterations 2.2949990E-04 7.6560974E-03 at 120iterations finished qdiffx linear iterations at : 08:56:27 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 2.2949990E-04 7.6560974E-03 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 08:56:28 7.939u 0.228s 0:08.44 96.5% 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 Sun Oct 9 2011 at 08:56:28 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 = 5497 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.254306 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): 3.845000 74.90900 ymin,ymax (A): 22.52600 84.18800 zmin,zma (A): 6.300000 70.56900 x,y,z range (A): 71.06400 61.66199 64.26900 scale (grids/A): 2.254306 object centre (A): 39.37700 53.35700 38.43450 number of atom coordinates read : 5497 total number of charged atoms : 5332 net assigned charge : -0.4999574 assigned positive charge : 825.9871 centred at (gu) : 90.28856 83.74050 86.10334 assigned negative charge : -826.4937 centred at (gu) : 89.51798 83.73221 85.67282 start vw surface at 0.1300000 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 231633 reading accessible surface arcs data from file ARCDAT no. of arc points read = 48321 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 98318 mr = 166701 m= 22511 mr = 75391 m= 2695 mr = 15704 m= 127 mr = 1601 m= 0 mr = 44 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 6804 time to turn everything in is 1.130000 number of dielectric boundary points 95843 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 107 iepsmp to db, and charging done at 1.230000 number of grid points assigned charge 42514 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) : 1.502871 object centre at (A) : 39.37700 53.35700 38.43450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2321296 0.1628767 midg,1,midg; midg,igrid,midg -6.3900076E-02 -8.5360713E-02 1,midg,midg; igrid,midg,midg -6.2012758E-02 0.5246238 gauss-seidel spectral radius is 0.9991780 estimated iterations to convergence 275 setup time was (sec) 1.370000 now iterating at: 08:56:29 rms-change max change #iterations 10.81272 336.8860 at 10iterations 6.261237 150.2461 at 20iterations 3.601880 82.72050 at 30iterations 2.058026 47.46447 at 40iterations 1.173045 22.61559 at 50iterations 0.6662234 13.13810 at 60iterations 0.3769730 8.698620 at 70iterations 0.2132932 3.819359 at 80iterations 0.1201926 2.481647 at 90iterations 6.7775361E-02 1.113678 at 100iterations 3.8203381E-02 0.7077980 at 110iterations 2.1429531E-02 0.3951941 at 120iterations 1.2052473E-02 0.2065172 at 130iterations 6.7797499E-03 0.1311436 at 140iterations 3.8048076E-03 6.7471981E-02 at 150iterations 2.1424456E-03 3.8934708E-02 at 160iterations 1.2033157E-03 2.3784637E-02 at 170iterations 6.7949324E-04 1.2235641E-02 at 180iterations finished qdiffx linear iterations at : 08:56:41 total time elapsed so far: 12.96000 # loops : 180 mean,max change (kT/e) : 6.7949324E-04 1.2235641E-02 energy calculations done at 12.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.10000 DelPhi exited at 08:56:41 13.103u 0.229s 0:13.60 97.9% 0+0k 0+0io 0pf+0w