Tue Oct 11 02:22:33 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 Tue Oct 11 2011 at 02:22:33 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2656 !!! WARNING: GLM 47 has a net charge of -0.0940 !!! WARNING: FMN 402 has a net charge of -2.0000 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: 0.6824760 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): -56.22300 -4.060000 ymin,ymax (A): -42.22700 3.574000 zmin,zma (A): -30.80800 17.49600 x,y,z range (A): 52.16300 45.80100 48.30400 scale (grids/A): 0.6824760 object centre (A): -30.14150 -19.32650 -6.656000 number of atom coordinates read : 2656 total number of charged atoms : 2517 net assigned charge : 3.406017 assigned positive charge : 408.9455 centred at (gu) : 88.72840 90.24979 89.83482 assigned negative charge : -405.5405 centred at (gu) : 89.02240 90.23502 89.80190 start vw surface at 0.1400000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8328 nv = 96 ne = 84 npr = 55037 no. pairs analyzed = 55037 no. exposed pairs = 3244 no. arc points = 22355 no. surface atoms = 1087 nbur = 1569 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 540 mr = 4776 m= 4 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 1 time to turn everything in is 0.3500000 number of dielectric boundary points 4008 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2140 ## 177 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 9689 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3793443E-09 2.5228202E-08 midg,1,midg; midg,igrid,midg 8.5033873E-09 2.0545583E-08 1,midg,midg; igrid,midg,midg 1.5218923E-07 -7.3072741E-08 gauss-seidel spectral radius is 0.9888726 estimated iterations to convergence 77 setup time was (sec) 0.6000000 now iterating at: 02:22:34 rms-change max change #iterations 0.2006370 28.42152 at 10iterations 2.3901748E-02 3.284309 at 20iterations 3.9057967E-03 0.6504364 at 30iterations 1.2615117E-03 0.2564583 at 40iterations 5.1878305E-04 0.1073265 at 50iterations finished qdiffx linear iterations at : 02:22:38 total time elapsed so far: 3.870000 # loops : 50 mean,max change (kT/e) : 5.1878305E-04 0.1073265 energy calculations done at 3.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.040000 DelPhi exited at 02:22:38 4.046u 0.285s 0:04.99 86.5% 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 02:22:39 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2656 !!! WARNING: GLM 47 has a net charge of -0.0940 !!! WARNING: FMN 402 has a net charge of -2.0000 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: 2.047428 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): -56.22300 -4.060000 ymin,ymax (A): -42.22700 3.574000 zmin,zma (A): -30.80800 17.49600 x,y,z range (A): 52.16300 45.80100 48.30400 scale (grids/A): 2.047428 object centre (A): -30.14150 -19.32650 -6.656000 number of atom coordinates read : 2656 total number of charged atoms : 2517 net assigned charge : 3.406017 assigned positive charge : 408.9455 centred at (gu) : 86.18437 90.74881 89.50357 assigned negative charge : -405.5405 centred at (gu) : 87.06709 90.70494 89.40548 start vw surface at 0.1700000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 88870 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22355 grid for indexing accessible points = 1.400000 m= 34510 mr = 62801 m= 6364 mr = 26053 m= 570 mr = 4215 m= 11 mr = 308 m= 0 mr = 0 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 296 time to turn everything in is 0.8000000 number of dielectric boundary points 36948 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 81 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 19957 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) : 0.6824760 object centre at (A) : -30.14150 -19.32650 -6.656000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.1440465E-02 -2.5420578E-02 midg,1,midg; midg,igrid,midg 2.0273425E-02 3.3869810E-02 1,midg,midg; igrid,midg,midg 9.0979129E-02 -5.6839135E-02 gauss-seidel spectral radius is 0.9988169 estimated iterations to convergence 230 setup time was (sec) 1.100000 now iterating at: 02:22:40 rms-change max change #iterations 5.048394 198.7975 at 10iterations 2.481402 80.44645 at 20iterations 1.222766 35.35811 at 30iterations 0.6033442 19.11568 at 40iterations 0.2980931 9.042768 at 50iterations 0.1472707 4.040999 at 60iterations 7.2912261E-02 2.057100 at 70iterations 3.6285307E-02 1.037006 at 80iterations 1.8211864E-02 0.5528831 at 90iterations 9.3411170E-03 0.2780075 at 100iterations 4.9373545E-03 0.1802635 at 110iterations 2.7850638E-03 9.9029541E-02 at 120iterations finished qdiffx linear iterations at : 02:22:48 total time elapsed so far: 9.440000 # loops : 120 mean,max change (kT/e) : 2.7850638E-03 9.9029541E-02 energy calculations done at 9.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.610000 DelPhi exited at 02:22:49 9.616u 0.291s 0:10.75 92.0% 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 02:22:49 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2656 !!! WARNING: GLM 47 has a net charge of -0.0940 !!! WARNING: FMN 402 has a net charge of -2.0000 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: 3.071142 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): -56.22300 -4.060000 ymin,ymax (A): -42.22700 3.574000 zmin,zma (A): -30.80800 17.49600 x,y,z range (A): 52.16300 45.80100 48.30400 scale (grids/A): 3.071142 object centre (A): -30.14150 -19.32650 -6.656000 number of atom coordinates read : 2656 total number of charged atoms : 2517 net assigned charge : 3.406017 assigned positive charge : 408.9455 centred at (gu) : 84.27644 91.12293 89.25523 assigned negative charge : -405.5405 centred at (gu) : 85.60054 91.05733 89.10804 start vw surface at 0.1700000 fill in re-entrant regions at 0.6900000 boundary points on vw surface= 205234 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22355 grid for indexing accessible points = 1.400000 m= 108161 mr = 151466 m= 43394 mr = 89743 m= 11776 mr = 35674 m= 2174 mr = 9040 m= 240 mr = 1551 m= 9 mr = 162 m= 0 mr = 0 time to grow re-entrant surface = 1.300000 no. cavity mid-points inaccessible to solvent = 1081 time to turn everything in is 2.110000 number of dielectric boundary points 83352 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.260000 number of grid points assigned charge 20136 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) : 2.047428 object centre at (A) : -30.14150 -19.32650 -6.656000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4481678 -0.3186329 midg,1,midg; midg,igrid,midg 0.1289549 0.4138486 1,midg,midg; igrid,midg,midg 0.5845602 -0.6819253 gauss-seidel spectral radius is 0.9993032 estimated iterations to convergence 299 setup time was (sec) 2.440000 now iterating at: 02:22:52 rms-change max change #iterations 11.37192 416.8909 at 10iterations 6.722528 138.5096 at 20iterations 3.969789 79.26861 at 30iterations 2.341671 46.98299 at 40iterations 1.378471 23.53828 at 50iterations 0.8113521 16.40448 at 60iterations 0.4759420 8.727451 at 70iterations 0.2795055 4.345147 at 80iterations 0.1637245 3.044407 at 90iterations 9.6259914E-02 1.789566 at 100iterations 5.6557059E-02 0.9720006 at 110iterations 3.3305671E-02 0.6591492 at 120iterations 1.9815518E-02 0.3556061 at 130iterations 1.1931186E-02 0.2506218 at 140iterations 7.3911017E-03 0.1600952 at 150iterations 4.7962912E-03 0.1121359 at 160iterations 3.3171242E-03 8.3297729E-02 at 170iterations 2.4504319E-03 6.4514160E-02 at 180iterations finished qdiffx linear iterations at : 02:23:06 total time elapsed so far: 16.32000 # loops : 180 mean,max change (kT/e) : 2.4504319E-03 6.4514160E-02 energy calculations done at 16.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.50000 DelPhi exited at 02:23:06 16.499u 0.304s 0:17.16 97.8% 0+0k 0+0io 0pf+0w