Sat Oct 8 14:43:28 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 14:43:28 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3034 !!! WARNING: NDP 318 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6387025 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): -12.18200 43.55600 ymin,ymax (A): -22.86300 22.31900 zmin,zma (A): -6.628000 47.82900 x,y,z range (A): 55.73800 45.18200 54.45700 scale (grids/A): 0.6387025 object centre (A): 15.68700 -0.2719994 20.60050 number of atom coordinates read : 3034 total number of charged atoms : 2887 net assigned charge : -1.999993 assigned positive charge : 453.5475 centred at (gu) : 88.83405 89.85121 91.25233 assigned negative charge : -455.5482 centred at (gu) : 88.79376 89.75263 91.22060 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8228 nv = 96 ne = 84 npr = 63695 no. pairs analyzed = 63695 no. exposed pairs = 3444 no. arc points = 24222 no. surface atoms = 1173 nbur = 1861 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 422 mr = 4796 m= 2 mr = 42 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 0.3600000 number of dielectric boundary points 3814 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2345 ## 211 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9982 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.3278617E-09 1.9119752E-09 midg,1,midg; midg,igrid,midg -1.6407915E-08 9.7673354E-09 1,midg,midg; igrid,midg,midg -1.0406472E-08 1.9335096E-09 gauss-seidel spectral radius is 0.9873331 estimated iterations to convergence 73 setup time was (sec) 0.6600000 now iterating at: 14:43:29 rms-change max change #iterations 0.1544091 22.40388 at 10iterations 1.5256909E-02 1.902103 at 20iterations 1.5662804E-03 0.1790371 at 30iterations 1.5888014E-04 2.0645142E-02 at 40iterations 1.7407418E-05 2.1820068E-03 at 50iterations finished qdiffx linear iterations at : 14:43:33 total time elapsed so far: 4.360000 # loops : 50 mean,max change (kT/e) : 1.7407418E-05 2.1820068E-03 energy calculations done at 4.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.540000 DelPhi exited at 14:43:33 4.545u 0.399s 0:05.28 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 Sat Oct 8 2011 at 14:43:33 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3034 !!! WARNING: NDP 318 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.916108 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): -12.18200 43.55600 ymin,ymax (A): -22.86300 22.31900 zmin,zma (A): -6.628000 47.82900 x,y,z range (A): 55.73800 45.18200 54.45700 scale (grids/A): 1.916108 object centre (A): 15.68700 -0.2719994 20.60050 number of atom coordinates read : 3034 total number of charged atoms : 2887 net assigned charge : -1.999993 assigned positive charge : 453.5475 centred at (gu) : 86.50175 89.55286 93.75642 assigned negative charge : -455.5482 centred at (gu) : 86.38103 89.25774 93.66160 start vw surface at 0.1100000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 89624 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24222 grid for indexing accessible points = 1.400000 m= 32115 mr = 64670 m= 4579 mr = 24060 m= 267 mr = 2758 m= 4 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6900000 number of dielectric boundary points 35012 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 162 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 22730 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) : 0.6387025 object centre at (A) : 15.68700 -0.2719994 20.60050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1448639E-02 3.7677153E-03 midg,1,midg; midg,igrid,midg -8.5551757E-03 1.6601993E-02 1,midg,midg; igrid,midg,midg -4.1198537E-02 1.2262495E-02 gauss-seidel spectral radius is 0.9986860 estimated iterations to convergence 219 setup time was (sec) 1.040000 now iterating at: 14:43:35 rms-change max change #iterations 4.670705 214.2183 at 10iterations 2.226086 83.49198 at 20iterations 1.056435 32.55883 at 30iterations 0.5040966 13.68209 at 40iterations 0.2398699 6.827956 at 50iterations 0.1142023 3.188241 at 60iterations 5.4277685E-02 1.444744 at 70iterations 2.5768926E-02 0.7740121 at 80iterations 1.2287969E-02 0.3352274 at 90iterations 5.8360794E-03 0.1732325 at 100iterations 2.7854112E-03 8.1233501E-02 at 110iterations 1.3261400E-03 4.3975830E-02 at 120iterations finished qdiffx linear iterations at : 14:43:45 total time elapsed so far: 10.68000 # loops : 120 mean,max change (kT/e) : 1.3261400E-03 4.3975830E-02 energy calculations done at 10.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.85000 DelPhi exited at 14:43:45 10.858u 0.469s 0:11.62 97.3% 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 Sat Oct 8 2011 at 14:43:45 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3034 !!! WARNING: NDP 318 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.874161 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): -12.18200 43.55600 ymin,ymax (A): -22.86300 22.31900 zmin,zma (A): -6.628000 47.82900 x,y,z range (A): 55.73800 45.18200 54.45700 scale (grids/A): 2.874161 object centre (A): 15.68700 -0.2719994 20.60050 number of atom coordinates read : 3034 total number of charged atoms : 2887 net assigned charge : -1.999993 assigned positive charge : 453.5475 centred at (gu) : 84.75246 89.32913 95.63429 assigned negative charge : -455.5482 centred at (gu) : 84.57155 88.88652 95.49220 start vw surface at 0.1200000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 207314 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24222 grid for indexing accessible points = 1.400000 m= 105835 mr = 156114 m= 36688 mr = 88018 m= 8211 mr = 29403 m= 1134 mr = 5924 m= 67 mr = 730 m= 1 mr = 27 m= 0 mr = 0 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.910000 number of dielectric boundary points 79034 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.030000 number of grid points assigned charge 23096 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) : 1.916108 object centre at (A) : 15.68700 -0.2719994 20.60050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9893385E-02 0.1606949 midg,1,midg; midg,igrid,midg -6.3764632E-02 0.1915514 1,midg,midg; igrid,midg,midg -0.5837872 0.1912461 gauss-seidel spectral radius is 0.9992766 estimated iterations to convergence 293 setup time was (sec) 2.220000 now iterating at: 14:43:48 rms-change max change #iterations 10.97283 444.4351 at 10iterations 6.453771 138.7618 at 20iterations 3.764116 77.20651 at 30iterations 2.198650 42.91328 at 40iterations 1.278100 24.07482 at 50iterations 0.7431579 12.67982 at 60iterations 0.4315375 6.894946 at 70iterations 0.2502993 4.557831 at 80iterations 0.1451438 2.399573 at 90iterations 8.4244020E-02 1.411486 at 100iterations 4.8645787E-02 0.7940059 at 110iterations 2.8166741E-02 0.4594765 at 120iterations 1.6328182E-02 0.2874193 at 130iterations 9.4455751E-03 0.1756783 at 140iterations 5.4643815E-03 8.8939667E-02 at 150iterations 3.1568354E-03 5.1754951E-02 at 160iterations 1.8292677E-03 3.0280113E-02 at 170iterations 1.0597379E-03 1.7946243E-02 at 180iterations finished qdiffx linear iterations at : 14:44:04 total time elapsed so far: 18.58000 # loops : 180 mean,max change (kT/e) : 1.0597379E-03 1.7946243E-02 energy calculations done at 18.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.73000 DelPhi exited at 14:44:05 18.737u 0.515s 0:19.55 98.4% 0+0k 0+0io 0pf+0w