Sun Oct 9 20:02:58 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 20:02:58 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5272 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.5411239 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): 3.310000 68.20200 ymin,ymax (A): -8.830000 53.48800 zmin,zma (A): -2.323000 63.46600 x,y,z range (A): 64.89201 62.31800 65.78900 scale (grids/A): 0.5411239 object centre (A): 35.75600 22.32900 30.57150 number of atom coordinates read : 5272 total number of charged atoms : 5108 net assigned charge : 0.7400498 assigned positive charge : 807.0686 centred at (gu) : 88.30669 89.10242 89.50954 assigned negative charge : -806.3345 centred at (gu) : 88.20012 89.11398 89.48877 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 10052 nv = 96 ne = 84 npr = 107005 no. pairs analyzed = 107005 no. exposed pairs = 6089 no. arc points = 41949 no. surface atoms = 2075 nbur = 3197 mkacc time = 0.2200000 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 = 1.596000 m= 402 mr = 5733 m= 3 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 4691 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4270 ## 538 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 13320 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6966288E-10 2.3457039E-10 midg,1,midg; midg,igrid,midg 2.1795749E-10 -4.5198949E-11 1,midg,midg; igrid,midg,midg -1.5769370E-09 7.2491102E-10 gauss-seidel spectral radius is 0.9825607 estimated iterations to convergence 62 setup time was (sec) 0.7000000 now iterating at: 20:02:59 rms-change max change #iterations 0.1016182 13.19706 at 10iterations 1.1861254E-02 1.547165 at 20iterations 4.6439539E-03 0.6697502 at 30iterations 2.1766599E-03 0.3277168 at 40iterations 1.0320744E-03 0.1581955 at 50iterations finished qdiffx linear iterations at : 20:03:01 total time elapsed so far: 3.100000 # loops : 50 mean,max change (kT/e) : 1.0320744E-03 0.1581955 energy calculations done at 3.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.270000 DelPhi exited at 20:03:02 3.278u 0.147s 0:03.97 85.8% 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 Sun Oct 9 2011 at 20:03:02 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5272 !!! WARNING: LLP 1 has a net charge of 1.7400 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.623372 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): 3.310000 68.20200 ymin,ymax (A): -8.830000 53.48800 zmin,zma (A): -2.323000 63.46600 x,y,z range (A): 64.89201 62.31800 65.78900 scale (grids/A): 1.623372 object centre (A): 35.75600 22.32900 30.57150 number of atom coordinates read : 5272 total number of charged atoms : 5108 net assigned charge : 0.7400498 assigned positive charge : 807.0686 centred at (gu) : 84.91898 87.30603 88.52708 assigned negative charge : -806.3345 centred at (gu) : 84.59996 87.34190 88.46622 start vw surface at 0.1900000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 113458 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41949 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 37954 mr = 82400 m= 4265 mr = 27379 m= 127 mr = 2215 m= 3 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 45 time to turn everything in is 0.7300000 number of dielectric boundary points 43790 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 464 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 39052 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) : 0.5411239 object centre at (A) : 35.75600 22.32900 30.57150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3950082E-02 -6.7269001E-03 midg,1,midg; midg,igrid,midg 1.2828561E-02 8.6505637E-03 1,midg,midg; igrid,midg,midg -2.5633149E-02 6.0270578E-03 gauss-seidel spectral radius is 0.9983729 estimated iterations to convergence 197 setup time was (sec) 0.9900000 now iterating at: 20:03:03 rms-change max change #iterations 4.672137 163.7120 at 10iterations 2.040389 61.34376 at 20iterations 0.8973801 24.00748 at 30iterations 0.3941453 11.63428 at 40iterations 0.1729302 5.152306 at 50iterations 7.7265494E-02 2.578098 at 60iterations 3.5412721E-02 1.000860 at 70iterations 1.7489005E-02 0.5929222 at 80iterations 9.8352879E-03 0.3021545 at 90iterations 6.3154818E-03 0.1993027 at 100iterations 4.4391109E-03 0.1338882 at 110iterations 3.2842453E-03 0.1016617 at 120iterations finished qdiffx linear iterations at : 20:03:09 total time elapsed so far: 7.010000 # loops : 120 mean,max change (kT/e) : 3.2842453E-03 0.1016617 energy calculations done at 7.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.170000 DelPhi exited at 20:03:10 7.176u 0.179s 0:07.68 95.5% 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 Sun Oct 9 2011 at 20:03:10 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: 267 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5272 !!! WARNING: LLP 1 has a net charge of 1.7400 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: 2.435057 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): 3.310000 68.20200 ymin,ymax (A): -8.830000 53.48800 zmin,zma (A): -2.323000 63.46600 x,y,z range (A): 64.89201 62.31800 65.78900 scale (grids/A): 2.435057 object centre (A): 35.75600 22.32900 30.57150 number of atom coordinates read : 5272 total number of charged atoms : 5108 net assigned charge : 0.7400498 assigned positive charge : 807.0686 centred at (gu) : 82.37815 85.95869 87.79033 assigned negative charge : -806.3345 centred at (gu) : 81.89998 86.01295 87.69936 start vw surface at 0.1900000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 264025 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41949 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 130856 mr = 200691 m= 39370 mr = 106783 m= 6713 mr = 30368 m= 558 mr = 4502 m= 10 mr = 306 m= 0 mr = 0 time to grow re-entrant surface = 1.110000 no. cavity mid-points inaccessible to solvent = 167 time to turn everything in is 1.820000 number of dielectric boundary points 98882 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 36 iepsmp to db, and charging done at 1.950000 number of grid points assigned charge 40797 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) : 1.623372 object centre at (A) : 35.75600 22.32900 30.57150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3087551 -0.1961605 midg,1,midg; midg,igrid,midg 0.1338311 2.6457699E-02 1,midg,midg; igrid,midg,midg -0.4580973 5.2543405E-02 gauss-seidel spectral radius is 0.9992383 estimated iterations to convergence 286 setup time was (sec) 2.110000 now iterating at: 20:03:12 rms-change max change #iterations 11.93839 315.5179 at 10iterations 6.989657 138.1866 at 20iterations 4.059054 77.63013 at 30iterations 2.352897 43.90947 at 40iterations 1.356555 22.80287 at 50iterations 0.7822107 14.24923 at 60iterations 0.4498881 7.849977 at 70iterations 0.2579731 4.139591 at 80iterations 0.1480427 2.824711 at 90iterations 8.5437037E-02 1.473510 at 100iterations 4.9300514E-02 0.8158493 at 110iterations 2.8808931E-02 0.5016327 at 120iterations 1.7214853E-02 0.3380547 at 130iterations 1.0707876E-02 0.2095642 at 140iterations 7.0413160E-03 0.1361237 at 150iterations 4.9690004E-03 9.5176697E-02 at 160iterations 3.7549143E-03 7.4188232E-02 at 170iterations 2.9774038E-03 5.6854248E-02 at 180iterations finished qdiffx linear iterations at : 20:03:22 total time elapsed so far: 12.71000 # loops : 180 mean,max change (kT/e) : 2.9774038E-03 5.6854248E-02 energy calculations done at 12.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.90000 DelPhi exited at 20:03:23 12.898u 0.177s 0:13.35 97.8% 0+0k 0+0io 0pf+0w