Sat Oct 8 11:37:26 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 8 2011 at 11:37:26 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 = 3314 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: 0.6223668 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): 32.87300 80.13400 ymin,ymax (A): 24.25300 81.45399 zmin,zma (A): -2.299000 46.17900 x,y,z range (A): 47.26101 57.20100 48.47800 scale (grids/A): 0.6223668 object centre (A): 56.50350 52.85350 21.94000 number of atom coordinates read : 3314 total number of charged atoms : 3164 net assigned charge : -3.499974 assigned positive charge : 503.2564 centred at (gu) : 90.70119 89.92075 90.80092 assigned negative charge : -506.7576 centred at (gu) : 90.48750 89.99319 90.78837 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8169 nv = 96 ne = 84 npr = 70415 no. pairs analyzed = 70415 no. exposed pairs = 3776 no. arc points = 25491 no. surface atoms = 1278 nbur = 2036 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 435 mr = 4837 m= 2 mr = 40 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 60 time to turn everything in is 0.3400000 number of dielectric boundary points 3729 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2452 ## 231 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 10240 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.6554504E-09 -2.3707094E-09 midg,1,midg; midg,igrid,midg 3.5693308E-09 -9.7865680E-09 1,midg,midg; igrid,midg,midg -2.0127187E-08 1.9008844E-08 gauss-seidel spectral radius is 0.9866779 estimated iterations to convergence 71 setup time was (sec) 0.5600000 now iterating at: 11:37:27 rms-change max change #iterations 0.1521055 21.86252 at 10iterations 1.4174246E-02 2.297153 at 20iterations 1.3520514E-03 0.1627388 at 30iterations 1.2872978E-04 1.6463280E-02 at 40iterations 1.3383139E-05 1.8157959E-03 at 50iterations finished qdiffx linear iterations at : 11:37:29 total time elapsed so far: 2.980000 # loops : 50 mean,max change (kT/e) : 1.3383139E-05 1.8157959E-03 energy calculations done at 2.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.160000 DelPhi exited at 11:37:30 3.162u 0.144s 0:03.98 82.9% 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 8 2011 at 11:37:30 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 = 3314 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.867100 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): 32.87300 80.13400 ymin,ymax (A): 24.25300 81.45399 zmin,zma (A): -2.299000 46.17900 x,y,z range (A): 47.26101 57.20100 48.47800 scale (grids/A): 1.867100 object centre (A): 56.50350 52.85350 21.94000 number of atom coordinates read : 3314 total number of charged atoms : 3164 net assigned charge : -3.499974 assigned positive charge : 503.2564 centred at (gu) : 92.10265 89.76157 92.40162 assigned negative charge : -506.7576 centred at (gu) : 91.46172 89.97894 92.36472 start vw surface at 0.1800000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 88442 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25491 grid for indexing accessible points = 1.400000 m= 33800 mr = 63533 m= 5747 mr = 26077 m= 284 mr = 3835 m= 1 mr = 83 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 4641 time to turn everything in is 0.6200000 number of dielectric boundary points 34746 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 170 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 24825 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) : 0.6223668 object centre at (A) : 56.50350 52.85350 21.94000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6777838E-02 -3.2675028E-02 midg,1,midg; midg,igrid,midg 9.7408863E-03 -2.8802229E-02 1,midg,midg; igrid,midg,midg -2.8023578E-02 3.0914556E-02 gauss-seidel spectral radius is 0.9986368 estimated iterations to convergence 215 setup time was (sec) 0.8800000 now iterating at: 11:37:31 rms-change max change #iterations 4.734175 183.4509 at 10iterations 2.211386 66.33554 at 20iterations 1.037763 33.50463 at 30iterations 0.4876962 14.66162 at 40iterations 0.2292128 7.572277 at 50iterations 0.1074929 3.438421 at 60iterations 5.0234251E-02 1.436572 at 70iterations 2.3652883E-02 0.6471205 at 80iterations 1.1133912E-02 0.3329926 at 90iterations 5.2027223E-03 0.1584597 at 100iterations 2.4544923E-03 7.1041107E-02 at 110iterations 1.1510714E-03 3.2660007E-02 at 120iterations finished qdiffx linear iterations at : 11:37:37 total time elapsed so far: 6.800000 # loops : 120 mean,max change (kT/e) : 1.1510714E-03 3.2660007E-02 energy calculations done at 6.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.970000 DelPhi exited at 11:37:38 6.977u 0.162s 0:07.62 93.5% 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 8 2011 at 11:37:38 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 = 3314 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.800651 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): 32.87300 80.13400 ymin,ymax (A): 24.25300 81.45399 zmin,zma (A): -2.299000 46.17900 x,y,z range (A): 47.26101 57.20100 48.47800 scale (grids/A): 2.800651 object centre (A): 56.50350 52.85350 21.94000 number of atom coordinates read : 3314 total number of charged atoms : 3164 net assigned charge : -3.499974 assigned positive charge : 503.2564 centred at (gu) : 93.15375 89.64223 93.60221 assigned negative charge : -506.7576 centred at (gu) : 92.19258 89.96826 93.54698 start vw surface at 0.1500000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 205021 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25491 grid for indexing accessible points = 1.400000 m= 107441 mr = 153888 m= 41995 mr = 89926 m= 10470 mr = 35062 m= 1393 mr = 8170 m= 60 mr = 1010 m= 1 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 15501 time to turn everything in is 1.510000 number of dielectric boundary points 78307 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 25312 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) : 1.867100 object centre at (A) : 56.50350 52.85350 21.94000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2485416 -0.3394207 midg,1,midg; midg,igrid,midg 4.1829903E-02 -5.8295786E-02 1,midg,midg; igrid,midg,midg -0.2790082 0.3305648 gauss-seidel spectral radius is 0.9992623 estimated iterations to convergence 291 setup time was (sec) 1.790000 now iterating at: 11:37:40 rms-change max change #iterations 11.03919 320.0570 at 10iterations 6.466294 129.8835 at 20iterations 3.743251 69.42856 at 30iterations 2.178021 41.37549 at 40iterations 1.258220 25.22615 at 50iterations 0.7269309 14.06385 at 60iterations 0.4188599 6.583726 at 70iterations 0.2416182 5.060611 at 80iterations 0.1391564 2.423790 at 90iterations 8.0227844E-02 1.266638 at 100iterations 4.6058767E-02 0.7462654 at 110iterations 2.6553832E-02 0.4501705 at 120iterations 1.5283635E-02 0.2627274 at 130iterations 8.7996963E-03 0.1424580 at 140iterations 5.0590863E-03 8.3279610E-02 at 150iterations 2.9193484E-03 4.7565460E-02 at 160iterations 1.6822882E-03 2.8164446E-02 at 170iterations 9.6908311E-04 1.7976761E-02 at 180iterations finished qdiffx linear iterations at : 11:37:49 total time elapsed so far: 11.15000 # loops : 180 mean,max change (kT/e) : 9.6908311E-04 1.7976761E-02 energy calculations done at 11.15000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.32000 DelPhi exited at 11:37:50 11.323u 0.188s 0:11.83 97.2% 0+0k 0+0io 0pf+0w