Tue Oct 11 06:09:05 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 Tue Oct 11 2011 at 06:09:05 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 = 2065 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: 0.7155204 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): 3.508000 46.14600 ymin,ymax (A): 0.6060001 41.42500 zmin,zma (A): -2.677000 47.07700 x,y,z range (A): 42.63800 40.81900 49.75400 scale (grids/A): 0.7155204 object centre (A): 24.82700 21.01550 22.20000 number of atom coordinates read : 2065 total number of charged atoms : 1937 net assigned charge : 7.500009 assigned positive charge : 312.8170 centred at (gu) : 90.45555 90.27835 90.59770 assigned negative charge : -305.3172 centred at (gu) : 90.64481 90.27279 90.64606 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7323 nv = 96 ne = 84 npr = 41296 no. pairs analyzed = 41296 no. exposed pairs = 2526 no. arc points = 17084 no. surface atoms = 861 nbur = 1204 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 498 mr = 4295 m= 4 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 3451 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1527 ## 149 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 7840 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.3897462E-08 5.4768485E-08 midg,1,midg; midg,igrid,midg 7.0334160E-08 8.4780680E-08 1,midg,midg; igrid,midg,midg 1.6917643E-07 -3.7911004E-08 gauss-seidel spectral radius is 0.9898148 estimated iterations to convergence 81 setup time was (sec) 0.5000000 now iterating at: 06:09:06 rms-change max change #iterations 0.2093891 28.66553 at 10iterations 2.6243336E-02 3.631784 at 20iterations 3.6430722E-03 0.5170135 at 30iterations 6.6207070E-04 8.7268829E-02 at 40iterations 1.9031469E-04 2.6092529E-02 at 50iterations finished qdiffx linear iterations at : 06:09:09 total time elapsed so far: 3.110000 # loops : 50 mean,max change (kT/e) : 1.9031469E-04 2.6092529E-02 energy calculations done at 3.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.300000 DelPhi exited at 06:09:09 3.300u 0.160s 0:03.78 91.5% 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 Tue Oct 11 2011 at 06:09:09 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 = 2065 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.146561 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): 3.508000 46.14600 ymin,ymax (A): 0.6060001 41.42500 zmin,zma (A): -2.677000 47.07700 x,y,z range (A): 42.63800 40.81900 49.75400 scale (grids/A): 2.146561 object centre (A): 24.82700 21.01550 22.20000 number of atom coordinates read : 2065 total number of charged atoms : 1937 net assigned charge : 7.500009 assigned positive charge : 312.8170 centred at (gu) : 91.36674 90.83487 91.79309 assigned negative charge : -305.3172 centred at (gu) : 91.93452 90.81826 91.93821 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 77057 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17084 grid for indexing accessible points = 1.400000 m= 31801 mr = 55228 m= 6399 mr = 24404 m= 554 mr = 4371 m= 7 mr = 242 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 31574 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 58 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 15398 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) : 0.7155204 object centre at (A) : 24.82700 21.01550 22.20000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9103368E-02 6.9940045E-02 midg,1,midg; midg,igrid,midg 6.8003028E-03 3.1651985E-02 1,midg,midg; igrid,midg,midg 4.6736535E-02 -9.6554530E-04 gauss-seidel spectral radius is 0.9988523 estimated iterations to convergence 234 setup time was (sec) 0.8900000 now iterating at: 06:09:10 rms-change max change #iterations 4.679568 161.8884 at 10iterations 2.327430 81.20148 at 20iterations 1.166633 38.54575 at 30iterations 0.5818338 16.36383 at 40iterations 0.2915848 9.691650 at 50iterations 0.1459994 4.631095 at 60iterations 7.3162541E-02 2.202071 at 70iterations 3.6643278E-02 1.133712 at 80iterations 1.8413480E-02 0.5946217 at 90iterations 9.3720527E-03 0.2943859 at 100iterations 4.7824322E-03 0.1433945 at 110iterations 2.5127917E-03 7.8004837E-02 at 120iterations finished qdiffx linear iterations at : 06:09:17 total time elapsed so far: 7.300000 # loops : 120 mean,max change (kT/e) : 2.5127917E-03 7.8004837E-02 energy calculations done at 7.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.490000 DelPhi exited at 06:09:17 7.491u 0.160s 0:08.08 94.6% 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 Tue Oct 11 2011 at 06:09:17 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 = 2065 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.219842 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): 3.508000 46.14600 ymin,ymax (A): 0.6060001 41.42500 zmin,zma (A): -2.677000 47.07700 x,y,z range (A): 42.63800 40.81900 49.75400 scale (grids/A): 3.219842 object centre (A): 24.82700 21.01550 22.20000 number of atom coordinates read : 2065 total number of charged atoms : 1937 net assigned charge : 7.500009 assigned positive charge : 312.8170 centred at (gu) : 92.05022 91.25233 92.68970 assigned negative charge : -305.3172 centred at (gu) : 92.90174 91.22744 92.90725 start vw surface at 0.1400000 fill in re-entrant regions at 0.8400000 boundary points on vw surface= 177457 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17084 grid for indexing accessible points = 1.400000 m= 98336 mr = 132535 m= 40950 mr = 82512 m= 12037 mr = 34041 m= 2321 mr = 9394 m= 167 mr = 1587 m= 2 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.9300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.880000 number of dielectric boundary points 71117 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.020000 number of grid points assigned charge 15496 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) : 2.146561 object centre at (A) : 24.82700 21.01550 22.20000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3796388 0.7281365 midg,1,midg; midg,igrid,midg -7.8662060E-04 0.2404492 1,midg,midg; igrid,midg,midg 0.3416147 8.3886959E-02 gauss-seidel spectral radius is 0.9992994 estimated iterations to convergence 298 setup time was (sec) 2.190000 now iterating at: 06:09:20 rms-change max change #iterations 10.27876 367.2752 at 10iterations 6.097370 122.3843 at 20iterations 3.607758 80.09595 at 30iterations 2.134107 44.05678 at 40iterations 1.256927 25.72927 at 50iterations 0.7396938 13.63601 at 60iterations 0.4355355 7.884245 at 70iterations 0.2560079 4.384468 at 80iterations 0.1502154 2.855358 at 90iterations 8.8373624E-02 1.513893 at 100iterations 5.1901735E-02 0.9397507 at 110iterations 3.0611726E-02 0.5295715 at 120iterations 1.8134732E-02 0.3318586 at 130iterations 1.0904616E-02 0.1962318 at 140iterations 6.7094285E-03 0.1214523 at 150iterations 4.2702085E-03 7.5614929E-02 at 160iterations 2.8747739E-03 5.4313660E-02 at 170iterations 2.0642884E-03 3.5758972E-02 at 180iterations finished qdiffx linear iterations at : 06:09:30 total time elapsed so far: 12.34000 # loops : 180 mean,max change (kT/e) : 2.0642884E-03 3.5758972E-02 energy calculations done at 12.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.53000 DelPhi exited at 06:09:30 12.533u 0.171s 0:13.01 97.6% 0+0k 0+0io 0pf+0w