Mon Oct 10 09:44:25 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+sph2.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 = amb2.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 Mon Oct 10 2011 at 09:44:26 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2877 !!! WARNING: HIT 226 has a net charge of 0.5140 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: 0.5722737 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): -17.97800 34.07000 ymin,ymax (A): -59.57800 -0.9680001 zmin,zma (A): -1.852000 60.35600 x,y,z range (A): 52.04800 58.61000 62.20800 scale (grids/A): 0.5722737 object centre (A): 8.046000 -30.27300 29.25200 number of atom coordinates read : 2877 total number of charged atoms : 2724 net assigned charge : 6.014014 assigned positive charge : 422.3728 centred at (gu) : 88.97301 88.15972 87.70387 assigned negative charge : -416.3593 centred at (gu) : 89.08005 88.02261 87.56985 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6383 nv = 96 ne = 84 npr = 55413 no. pairs analyzed = 55413 no. exposed pairs = 4330 no. arc points = 31567 no. surface atoms = 1446 nbur = 1431 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 = 1.484000 m= 297 mr = 2771 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 0.3200000 number of dielectric boundary points 3901 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3136 ## 365 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8077 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9170709E-09 1.8356150E-09 midg,1,midg; midg,igrid,midg -1.7822174E-09 2.0702429E-09 1,midg,midg; igrid,midg,midg 3.4886471E-09 -4.8224374E-10 gauss-seidel spectral radius is 0.9842547 estimated iterations to convergence 65 setup time was (sec) 0.5700000 now iterating at: 09:44:26 rms-change max change #iterations 8.7938324E-02 15.28753 at 10iterations 6.4653242E-03 1.053146 at 20iterations 4.9127551E-04 7.4390411E-02 at 30iterations 4.1172632E-05 6.1435699E-03 at 40iterations 4.9323003E-06 6.0653687E-04 at 50iterations finished qdiffx linear iterations at : 09:44:29 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 4.9323003E-06 6.0653687E-04 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.420000 DelPhi exited at 09:44:30 3.420u 0.175s 0:04.11 87.3% 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 Mon Oct 10 2011 at 09:44:30 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2877 !!! WARNING: HIT 226 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.716821 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): -17.97800 34.07000 ymin,ymax (A): -59.57800 -0.9680001 zmin,zma (A): -1.852000 60.35600 x,y,z range (A): 52.04800 58.61000 62.20800 scale (grids/A): 1.716821 object centre (A): 8.046000 -30.27300 29.25200 number of atom coordinates read : 2877 total number of charged atoms : 2724 net assigned charge : 6.014014 assigned positive charge : 422.3728 centred at (gu) : 86.91838 84.47835 83.11103 assigned negative charge : -416.3593 centred at (gu) : 87.23984 84.06760 82.70920 start vw surface at 0.2100000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 68288 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31567 grid for indexing accessible points = 1.400000 m= 20848 mr = 41408 m= 2471 mr = 13002 m= 98 mr = 1036 m= 2 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 36250 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 292 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 21123 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) : 0.5722737 object centre at (A) : 8.046000 -30.27300 29.25200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9194411E-02 7.0891652E-04 midg,1,midg; midg,igrid,midg 1.8656684E-02 3.2633964E-02 1,midg,midg; igrid,midg,midg 1.0027912E-02 6.9028544E-03 gauss-seidel spectral radius is 0.9983753 estimated iterations to convergence 197 setup time was (sec) 0.8500000 now iterating at: 09:44:31 rms-change max change #iterations 3.612354 203.4271 at 10iterations 1.567686 66.15836 at 20iterations 0.6852807 23.43470 at 30iterations 0.2988260 11.98678 at 40iterations 0.1305983 5.605194 at 50iterations 5.6849223E-02 2.183698 at 60iterations 2.4747284E-02 0.8371048 at 70iterations 1.0840300E-02 0.3871689 at 80iterations 4.7285650E-03 0.1708641 at 90iterations 2.0698169E-03 7.5020790E-02 at 100iterations 9.0232433E-04 3.3037186E-02 at 110iterations 3.9580863E-04 1.3581753E-02 at 120iterations finished qdiffx linear iterations at : 09:44:37 total time elapsed so far: 7.290000 # loops : 120 mean,max change (kT/e) : 3.9580863E-04 1.3581753E-02 energy calculations done at 7.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.470000 DelPhi exited at 09:44:38 7.477u 0.215s 0:08.10 94.8% 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 Mon Oct 10 2011 at 09:44:38 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: 300 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2877 !!! WARNING: HIT 226 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.575232 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): -17.97800 34.07000 ymin,ymax (A): -59.57800 -0.9680001 zmin,zma (A): -1.852000 60.35600 x,y,z range (A): 52.04800 58.61000 62.20800 scale (grids/A): 2.575232 object centre (A): 8.046000 -30.27300 29.25200 number of atom coordinates read : 2877 total number of charged atoms : 2724 net assigned charge : 6.014014 assigned positive charge : 422.3728 centred at (gu) : 85.37751 81.71741 79.66649 assigned negative charge : -416.3593 centred at (gu) : 85.85976 81.10133 79.06367 start vw surface at 0.2200000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 157846 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31567 grid for indexing accessible points = 1.400000 m= 69568 mr = 102506 m= 21329 mr = 51392 m= 3787 mr = 14901 m= 299 mr = 2115 m= 6 mr = 108 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.230000 number of dielectric boundary points 81813 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 21787 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) : 1.716821 object centre at (A) : 8.046000 -30.27300 29.25200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.5259954 1.5747285E-02 midg,1,midg; midg,igrid,midg 0.3883658 0.4138454 1,midg,midg; igrid,midg,midg 4.1524183E-02 9.8750055E-02 gauss-seidel spectral radius is 0.9992129 estimated iterations to convergence 281 setup time was (sec) 1.510000 now iterating at: 09:44:40 rms-change max change #iterations 9.315488 326.4749 at 10iterations 5.503407 164.5656 at 20iterations 3.204948 74.50725 at 30iterations 1.847983 54.62424 at 40iterations 1.059892 28.52623 at 50iterations 0.6080174 16.90780 at 60iterations 0.3470908 8.753046 at 70iterations 0.1976846 4.955578 at 80iterations 0.1121403 2.501210 at 90iterations 6.3553840E-02 1.280212 at 100iterations 3.6114354E-02 0.7733288 at 110iterations 2.0448741E-02 0.4830351 at 120iterations 1.1575895E-02 0.2836952 at 130iterations 6.5561174E-03 0.1291628 at 140iterations 3.6947799E-03 7.3375702E-02 at 150iterations 2.0864888E-03 4.6054840E-02 at 160iterations 1.1798086E-03 2.2438049E-02 at 170iterations 6.6521514E-04 1.2808800E-02 at 180iterations finished qdiffx linear iterations at : 09:44:49 total time elapsed so far: 11.03000 # loops : 180 mean,max change (kT/e) : 6.6521514E-04 1.2808800E-02 energy calculations done at 11.03000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.21000 DelPhi exited at 09:44:50 11.208u 0.165s 0:11.64 97.5% 0+0k 0+0io 0pf+0w