Sun Oct 9 21:06:18 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 21:06:18 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 = 3174 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: 0.6086615 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): -21.12900 31.92400 ymin,ymax (A): 23.39400 81.88300 zmin,zma (A): -16.71700 38.42100 x,y,z range (A): 53.05300 58.48899 55.13800 scale (grids/A): 0.6086615 object centre (A): 5.397500 52.63850 10.85200 number of atom coordinates read : 3174 total number of charged atoms : 3026 net assigned charge : 4.500013 assigned positive charge : 478.8007 centred at (gu) : 89.09581 88.15783 89.21170 assigned negative charge : -474.3020 centred at (gu) : 89.17152 88.11745 89.16264 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7884 nv = 96 ne = 84 npr = 62534 no. pairs analyzed = 62534 no. exposed pairs = 4284 no. arc points = 31024 no. surface atoms = 1428 nbur = 1746 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 422 mr = 3961 m= 3 mr = 43 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 0.3900000 number of dielectric boundary points 4305 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3160 ## 342 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 9867 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.7188388E-10 4.5199786E-09 midg,1,midg; midg,igrid,midg 2.5090655E-10 3.2603975E-09 1,midg,midg; igrid,midg,midg 8.4594474E-09 -1.4832432E-09 gauss-seidel spectral radius is 0.9860862 estimated iterations to convergence 69 setup time was (sec) 0.6600000 now iterating at: 21:06:19 rms-change max change #iterations 0.1265225 18.73974 at 10iterations 1.1072214E-02 1.689307 at 20iterations 9.9209766E-04 0.1328106 at 30iterations 9.1269874E-05 1.2907982E-02 at 40iterations 1.1246247E-05 1.6698837E-03 at 50iterations finished qdiffx linear iterations at : 21:06:23 total time elapsed so far: 4.530000 # loops : 50 mean,max change (kT/e) : 1.1246247E-05 1.6698837E-03 energy calculations done at 4.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.720000 DelPhi exited at 21:06:24 4.722u 0.382s 0:05.47 93.2% 0+0k 0+0io 5pf+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 21:06:24 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 = 3174 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: 1.825985 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): -21.12900 31.92400 ymin,ymax (A): 23.39400 81.88300 zmin,zma (A): -16.71700 38.42100 x,y,z range (A): 53.05300 58.48899 55.13800 scale (grids/A): 1.825985 object centre (A): 5.397500 52.63850 10.85200 number of atom coordinates read : 3174 total number of charged atoms : 3026 net assigned charge : 4.500013 assigned positive charge : 478.8007 centred at (gu) : 87.28632 84.47266 87.63400 assigned negative charge : -474.3020 centred at (gu) : 87.51418 84.35217 87.48746 start vw surface at 0.1300000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 85605 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31024 grid for indexing accessible points = 1.400000 m= 28320 mr = 56496 m= 3983 mr = 19592 m= 214 mr = 2256 m= 2 mr = 58 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 288 time to turn everything in is 0.7000000 number of dielectric boundary points 39722 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 236 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 23655 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) : 0.6086615 object centre at (A) : 5.397500 52.63850 10.85200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3250235E-02 1.5883514E-03 midg,1,midg; midg,igrid,midg 3.4504812E-02 5.5139605E-03 1,midg,midg; igrid,midg,midg 1.4368434E-02 -1.6333424E-03 gauss-seidel spectral radius is 0.9985920 estimated iterations to convergence 211 setup time was (sec) 1.070000 now iterating at: 21:06:26 rms-change max change #iterations 4.336570 162.0357 at 10iterations 1.999941 67.55233 at 20iterations 0.9231119 29.04625 at 30iterations 0.4253503 12.93241 at 40iterations 0.1963772 5.910233 at 50iterations 9.0667665E-02 2.778606 at 60iterations 4.1806046E-02 1.255358 at 70iterations 1.9389793E-02 0.6094481 at 80iterations 8.9673912E-03 0.2900047 at 90iterations 4.1461620E-03 0.1218529 at 100iterations 1.9127553E-03 5.6233406E-02 at 110iterations 8.8871026E-04 2.8877258E-02 at 120iterations finished qdiffx linear iterations at : 21:06:36 total time elapsed so far: 11.04000 # loops : 120 mean,max change (kT/e) : 8.8871026E-04 2.8877258E-02 energy calculations done at 11.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.20000 DelPhi exited at 21:06:36 11.208u 0.461s 0:12.19 95.6% 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 21:06:36 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 = 3174 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: 2.738977 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): -21.12900 31.92400 ymin,ymax (A): 23.39400 81.88300 zmin,zma (A): -16.71700 38.42100 x,y,z range (A): 53.05300 58.48899 55.13800 scale (grids/A): 2.738977 object centre (A): 5.397500 52.63850 10.85200 number of atom coordinates read : 3174 total number of charged atoms : 3026 net assigned charge : 4.500013 assigned positive charge : 478.8007 centred at (gu) : 85.92931 81.70863 86.45087 assigned negative charge : -474.3020 centred at (gu) : 86.27113 81.52808 86.23123 start vw surface at 0.1200000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 198282 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31024 grid for indexing accessible points = 1.400000 m= 93536 mr = 138570 m= 30883 mr = 73547 m= 6878 mr = 23394 m= 928 mr = 4846 m= 45 mr = 598 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 1.100000 no. cavity mid-points inaccessible to solvent = 1152 time to turn everything in is 1.770000 number of dielectric boundary points 89593 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.920000 number of grid points assigned charge 24199 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) : 1.825985 object centre at (A) : 5.397500 52.63850 10.85200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3135141 -1.7727254E-03 midg,1,midg; midg,igrid,midg 0.9734470 0.1453331 1,midg,midg; igrid,midg,midg 0.2172101 -3.7566762E-02 gauss-seidel spectral radius is 0.9992763 estimated iterations to convergence 293 setup time was (sec) 2.120000 now iterating at: 21:06:39 rms-change max change #iterations 10.65499 307.0957 at 10iterations 6.392940 149.8156 at 20iterations 3.788051 82.30775 at 30iterations 2.235079 46.19040 at 40iterations 1.311231 25.45002 at 50iterations 0.7666394 15.27941 at 60iterations 0.4484364 9.305433 at 70iterations 0.2610681 5.177556 at 80iterations 0.1518206 3.325291 at 90iterations 8.8285513E-02 1.820488 at 100iterations 5.1238596E-02 0.9533100 at 110iterations 2.9756496E-02 0.5401690 at 120iterations 1.7271368E-02 0.3171399 at 130iterations 9.9934544E-03 0.1885281 at 140iterations 5.7954346E-03 0.1013346 at 150iterations 3.3571678E-03 5.1853180E-02 at 160iterations 1.9419629E-03 3.4103394E-02 at 170iterations 1.1250969E-03 1.9149780E-02 at 180iterations finished qdiffx linear iterations at : 21:06:56 total time elapsed so far: 19.56000 # loops : 180 mean,max change (kT/e) : 1.1250969E-03 1.9149780E-02 energy calculations done at 19.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.74000 DelPhi exited at 21:06:57 19.742u 0.497s 0:20.60 98.2% 0+0k 0+0io 0pf+0w