Sun Oct 9 18:48:45 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 Sun Oct 9 2011 at 18:48:45 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3329 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5120534 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): -8.201000 61.32300 ymin,ymax (A): -18.56900 35.75400 zmin,zma (A): 18.56200 69.57100 x,y,z range (A): 69.52400 54.32300 51.00900 scale (grids/A): 0.5120534 object centre (A): 26.56100 8.592501 44.06650 number of atom coordinates read : 3329 total number of charged atoms : 3181 net assigned charge : 9.500021 assigned positive charge : 513.1077 centred at (gu) : 90.59763 90.63248 89.93119 assigned negative charge : -503.6090 centred at (gu) : 90.63522 90.67455 89.87526 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5479 nv = 96 ne = 84 npr = 66437 no. pairs analyzed = 66437 no. exposed pairs = 4327 no. arc points = 29936 no. surface atoms = 1455 nbur = 1874 mkacc time = 0.1800000 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 = 1.680000 m= 210 mr = 2703 m= 0 mr = 3 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 2983 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3043 ## 474 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 7447 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.5901327E-11 2.4856350E-10 midg,1,midg; midg,igrid,midg 1.9225599E-10 7.3026252E-11 1,midg,midg; igrid,midg,midg 1.8664945E-10 8.2739073E-11 gauss-seidel spectral radius is 0.9803909 estimated iterations to convergence 59 setup time was (sec) 0.6600000 now iterating at: 18:48:46 rms-change max change #iterations 5.6559548E-02 9.850204 at 10iterations 3.3637113E-03 0.6474752 at 20iterations 2.9809505E-04 6.5052032E-02 at 30iterations 8.0366925E-05 1.2195587E-02 at 40iterations 3.6737223E-05 6.2937737E-03 at 50iterations finished qdiffx linear iterations at : 18:48:49 total time elapsed so far: 3.450000 # loops : 50 mean,max change (kT/e) : 3.6737223E-05 6.2937737E-03 energy calculations done at 3.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.660000 DelPhi exited at 18:48:49 3.659u 0.164s 0:04.13 92.2% 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 18:48:49 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3329 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.536160 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): -8.201000 61.32300 ymin,ymax (A): -18.56900 35.75400 zmin,zma (A): 18.56200 69.57100 x,y,z range (A): 69.52400 54.32300 51.00900 scale (grids/A): 1.536160 object centre (A): 26.56100 8.592501 44.06650 number of atom coordinates read : 3329 total number of charged atoms : 3181 net assigned charge : 9.500021 assigned positive charge : 513.1077 centred at (gu) : 91.79199 91.89664 89.79254 assigned negative charge : -503.6090 centred at (gu) : 91.90516 92.02309 89.62560 start vw surface at 0.1900000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 61877 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29936 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 17830 mr = 41183 m= 1554 mr = 11623 m= 26 mr = 622 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 266 time to turn everything in is 0.5300000 number of dielectric boundary points 27860 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 361 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 23885 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) : 0.5120534 object centre at (A) : 26.56100 8.592501 44.06650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.3087447E-04 2.9913601E-03 midg,1,midg; midg,igrid,midg 5.0555114E-03 1.6260978E-03 1,midg,midg; igrid,midg,midg 2.2805154E-02 8.1075439E-03 gauss-seidel spectral radius is 0.9979680 estimated iterations to convergence 176 setup time was (sec) 0.8300000 now iterating at: 18:48:50 rms-change max change #iterations 3.101665 142.8618 at 10iterations 1.224466 48.52710 at 20iterations 0.4844602 18.83053 at 30iterations 0.1922714 7.389419 at 40iterations 7.6529227E-02 3.130650 at 50iterations 3.0319126E-02 1.084890 at 60iterations 1.2038668E-02 0.4663959 at 70iterations 4.8127957E-03 0.1889763 at 80iterations 1.9257308E-03 7.6669693E-02 at 90iterations 7.8733137E-04 2.9430389E-02 at 100iterations 3.3759218E-04 1.3359547E-02 at 110iterations 1.6619620E-04 6.7067146E-03 at 120iterations finished qdiffx linear iterations at : 18:48:57 total time elapsed so far: 7.370000 # loops : 120 mean,max change (kT/e) : 1.6619620E-04 6.7067146E-03 energy calculations done at 7.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.590000 DelPhi exited at 18:48:58 7.588u 0.205s 0:08.16 95.3% 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 Sun Oct 9 2011 at 18:48:58 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: 266 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3329 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.304240 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): -8.201000 61.32300 ymin,ymax (A): -18.56900 35.75400 zmin,zma (A): 18.56200 69.57100 x,y,z range (A): 69.52400 54.32300 51.00900 scale (grids/A): 2.304240 object centre (A): 26.56100 8.592501 44.06650 number of atom coordinates read : 3329 total number of charged atoms : 3181 net assigned charge : 9.500021 assigned positive charge : 513.1077 centred at (gu) : 92.68792 92.84474 89.68850 assigned negative charge : -503.6090 centred at (gu) : 92.85758 93.03452 89.43834 start vw surface at 0.2000000 fill in re-entrant regions at 0.4200000 boundary points on vw surface= 143950 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29936 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 63483 mr = 101344 m= 16410 mr = 48843 m= 2130 mr = 11849 m= 114 mr = 1215 m= 1 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 898 time to turn everything in is 1.180000 number of dielectric boundary points 62792 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 46 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 25382 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) : 1.536160 object centre at (A) : 26.56100 8.592501 44.06650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.7162014E-03 4.5903526E-02 midg,1,midg; midg,igrid,midg 7.7155799E-02 -1.0855420E-02 1,midg,midg; igrid,midg,midg 0.7132400 3.2918684E-02 gauss-seidel spectral radius is 0.9990713 estimated iterations to convergence 259 setup time was (sec) 1.510000 now iterating at: 18:48:59 rms-change max change #iterations 8.398799 304.4356 at 10iterations 4.628836 110.8605 at 20iterations 2.533468 72.36703 at 30iterations 1.382951 35.90372 at 40iterations 0.7504062 16.77051 at 50iterations 0.4074944 9.812654 at 60iterations 0.2202701 5.040619 at 70iterations 0.1192582 2.974758 at 80iterations 6.4230070E-02 1.517080 at 90iterations 3.4827087E-02 0.8344588 at 100iterations 1.8798986E-02 0.4390621 at 110iterations 1.0121863E-02 0.2579842 at 120iterations 5.4638344E-03 0.1223650 at 130iterations 2.9384030E-03 6.8645477E-02 at 140iterations 1.5865873E-03 3.5079956E-02 at 150iterations 8.5536571E-04 2.0037651E-02 at 160iterations 4.6284453E-04 1.0802269E-02 at 170iterations 2.5263015E-04 5.4509640E-03 at 180iterations finished qdiffx linear iterations at : 18:49:09 total time elapsed so far: 11.70000 # loops : 180 mean,max change (kT/e) : 2.5263015E-04 5.4509640E-03 energy calculations done at 11.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.92000 DelPhi exited at 18:49:10 11.923u 0.210s 0:12.41 97.7% 0+0k 0+0io 0pf+0w