Tue Oct 11 08:03:29 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 08:03:29 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3195 !!! WARNING: HIT 150 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5038211 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): 10.66600 73.89100 ymin,ymax (A): -6.751000 63.90900 zmin,zma (A): -9.148000 41.60700 x,y,z range (A): 63.22500 70.66000 50.75500 scale (grids/A): 0.5038211 object centre (A): 42.27850 28.57900 16.22950 number of atom coordinates read : 3195 total number of charged atoms : 3050 net assigned charge : 15.01401 assigned positive charge : 482.0354 centred at (gu) : 89.96863 91.74702 89.24384 assigned negative charge : -467.0229 centred at (gu) : 90.08856 91.81030 89.17647 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 5274 nv = 96 ne = 84 npr = 59818 no. pairs analyzed = 59818 no. exposed pairs = 4414 no. arc points = 32253 no. surface atoms = 1493 nbur = 1702 mkacc time = 0.1700000 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 = 1.708000 m= 164 mr = 2326 m= 1 mr = 2 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 3111 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3194 ## 540 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 7102 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.7939947E-11 1.9894549E-10 midg,1,midg; midg,igrid,midg 1.5066683E-10 1.2099773E-10 1,midg,midg; igrid,midg,midg 3.0962910E-10 5.1323629E-12 gauss-seidel spectral radius is 0.9797605 estimated iterations to convergence 58 setup time was (sec) 0.6600000 now iterating at: 08:03:30 rms-change max change #iterations 4.8824269E-02 9.318001 at 10iterations 2.5988340E-03 0.5101433 at 20iterations 1.4349447E-04 2.7742386E-02 at 30iterations 8.3417817E-06 1.4667511E-03 at 40iterations 6.2098877E-07 8.0108643E-05 at 50iterations finished qdiffx linear iterations at : 08:03:33 total time elapsed so far: 4.020000 # loops : 50 mean,max change (kT/e) : 6.2098877E-07 8.0108643E-05 energy calculations done at 4.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.210000 DelPhi exited at 08:03:34 4.209u 0.265s 0:04.86 91.7% 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 08:03:34 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3195 !!! WARNING: HIT 150 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.511463 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): 10.66600 73.89100 ymin,ymax (A): -6.751000 63.90900 zmin,zma (A): -9.148000 41.60700 x,y,z range (A): 63.22500 70.66000 50.75500 scale (grids/A): 1.511463 object centre (A): 42.27850 28.57900 16.22950 number of atom coordinates read : 3195 total number of charged atoms : 3050 net assigned charge : 15.01401 assigned positive charge : 482.0354 centred at (gu) : 89.90511 95.24023 87.73047 assigned negative charge : -467.0229 centred at (gu) : 90.26540 95.43045 87.52913 start vw surface at 0.1800000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 59170 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32253 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 15481 mr = 36760 m= 1134 mr = 9665 m= 23 mr = 362 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 220 time to turn everything in is 0.5700000 number of dielectric boundary points 29021 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 489 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 22853 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) : 0.5038211 object centre at (A) : 42.27850 28.57900 16.22950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.8157739E-03 4.2210878E-03 midg,1,midg; midg,igrid,midg 1.2447732E-02 -8.0105365E-04 1,midg,midg; igrid,midg,midg 1.6480530E-02 4.7306223E-03 gauss-seidel spectral radius is 0.9978984 estimated iterations to convergence 174 setup time was (sec) 0.8700000 now iterating at: 08:03:35 rms-change max change #iterations 2.846443 174.6026 at 10iterations 1.104790 51.45084 at 20iterations 0.4290386 17.84816 at 30iterations 0.1674667 6.780411 at 40iterations 6.4685121E-02 2.640093 at 50iterations 2.5226118E-02 1.018575 at 60iterations 9.7627193E-03 0.3770752 at 70iterations 3.8183969E-03 0.1533458 at 80iterations 1.4873662E-03 5.8239698E-02 at 90iterations 5.7691237E-04 2.2469521E-02 at 100iterations 2.2568369E-04 9.5005035E-03 at 110iterations 8.7825334E-05 3.6156178E-03 at 120iterations finished qdiffx linear iterations at : 08:03:43 total time elapsed so far: 9.200000 # loops : 120 mean,max change (kT/e) : 8.7825334E-05 3.6156178E-03 energy calculations done at 9.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.390000 DelPhi exited at 08:03:44 9.388u 0.291s 0:09.98 96.8% 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 08:03:44 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: 311 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3195 !!! WARNING: HIT 150 has a net charge of 0.5140 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: 2.267195 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): 10.66600 73.89100 ymin,ymax (A): -6.751000 63.90900 zmin,zma (A): -9.148000 41.60700 x,y,z range (A): 63.22500 70.66000 50.75500 scale (grids/A): 2.267195 object centre (A): 42.27850 28.57900 16.22950 number of atom coordinates read : 3195 total number of charged atoms : 3050 net assigned charge : 15.01401 assigned positive charge : 482.0354 centred at (gu) : 89.85748 97.85995 86.59547 assigned negative charge : -467.0229 centred at (gu) : 90.39822 98.14561 86.29356 start vw surface at 0.1700000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 137853 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32253 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 55797 mr = 91340 m= 12771 mr = 41605 m= 1398 mr = 8708 m= 52 mr = 678 m= 1 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 735 time to turn everything in is 1.290000 number of dielectric boundary points 65534 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 66 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 24327 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) : 1.511463 object centre at (A) : 42.27850 28.57900 16.22950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1151349 6.5189697E-02 midg,1,midg; midg,igrid,midg 0.1964941 -7.5987279E-02 1,midg,midg; igrid,midg,midg 0.2915967 8.2290463E-02 gauss-seidel spectral radius is 0.9990466 estimated iterations to convergence 256 setup time was (sec) 1.610000 now iterating at: 08:03:46 rms-change max change #iterations 7.875433 253.1440 at 10iterations 4.309464 126.6218 at 20iterations 2.352405 58.54267 at 30iterations 1.268199 29.17665 at 40iterations 0.6836175 17.50875 at 50iterations 0.3668070 8.334017 at 60iterations 0.1965380 4.955850 at 70iterations 0.1051099 2.435532 at 80iterations 5.6190122E-02 1.300997 at 90iterations 2.9853651E-02 0.7134151 at 100iterations 1.5908530E-02 0.3781509 at 110iterations 8.4899608E-03 0.2051468 at 120iterations 4.5119934E-03 0.1008186 at 130iterations 2.3975219E-03 5.0043583E-02 at 140iterations 1.2766363E-03 2.8785706E-02 at 150iterations 6.7741476E-04 1.4854431E-02 at 160iterations 3.6015347E-04 8.0409050E-03 at 170iterations 1.9158468E-04 4.2381287E-03 at 180iterations finished qdiffx linear iterations at : 08:04:00 total time elapsed so far: 15.22000 # loops : 180 mean,max change (kT/e) : 1.9158468E-04 4.2381287E-03 energy calculations done at 15.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.40000 DelPhi exited at 08:04:01 15.401u 0.322s 0:16.56 94.9% 0+0k 0+0io 0pf+0w