Sun Oct 9 19:11:59 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 19:11:59 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 = 5129 !!! 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5241230 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): 3.341000 68.16000 ymin,ymax (A): -8.724000 59.19900 zmin,zma (A): -2.280000 62.00600 x,y,z range (A): 64.81900 67.92300 64.28600 scale (grids/A): 0.5241230 object centre (A): 35.75050 25.23750 29.86300 number of atom coordinates read : 5129 total number of charged atoms : 4954 net assigned charge : 3.240037 assigned positive charge : 781.7942 centred at (gu) : 87.73634 88.14586 89.29253 assigned negative charge : -778.5596 centred at (gu) : 87.60737 88.16128 89.29617 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 9063 nv = 96 ne = 84 npr = 103693 no. pairs analyzed = 103693 no. exposed pairs = 6038 no. arc points = 40740 no. surface atoms = 2061 nbur = 3068 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 = 1.652000 m= 354 mr = 5093 m= 0 mr = 13 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 4311 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4091 ## 549 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 12106 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3687827E-10 6.6010239E-11 midg,1,midg; midg,igrid,midg 2.7779176E-10 1.3976149E-11 1,midg,midg; igrid,midg,midg -1.0002700E-09 4.0218179E-10 gauss-seidel spectral radius is 0.9814017 estimated iterations to convergence 61 setup time was (sec) 0.5300000 now iterating at: 19:12:00 rms-change max change #iterations 8.5341059E-02 10.96702 at 10iterations 1.2709304E-02 1.946312 at 20iterations 5.1906048E-03 0.8236237 at 30iterations 2.2859382E-03 0.3550949 at 40iterations 1.0140474E-03 0.1536789 at 50iterations finished qdiffx linear iterations at : 19:12:03 total time elapsed so far: 3.450000 # loops : 50 mean,max change (kT/e) : 1.0140474E-03 0.1536789 energy calculations done at 3.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 19:12:03 3.590u 0.183s 0:04.08 92.4% 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 19:12:03 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 = 5129 !!! 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.572369 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): 3.341000 68.16000 ymin,ymax (A): -8.724000 59.19900 zmin,zma (A): -2.280000 62.00600 x,y,z range (A): 64.81900 67.92300 64.28600 scale (grids/A): 1.572369 object centre (A): 35.75050 25.23750 29.86300 number of atom coordinates read : 5129 total number of charged atoms : 4954 net assigned charge : 3.240037 assigned positive charge : 781.7942 centred at (gu) : 83.20786 84.43645 87.87622 assigned negative charge : -778.5596 centred at (gu) : 82.82230 84.48383 87.88873 start vw surface at 0.1400000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 103490 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40740 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 33285 mr = 74754 m= 3405 mr = 23386 m= 75 mr = 1667 m= 0 mr = 3 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 40445 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 477 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.5900000 number of grid points assigned charge 37487 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) : 0.5241230 object centre at (A) : 35.75050 25.23750 29.86300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.0548081E-03 -1.3076933E-02 midg,1,midg; midg,igrid,midg 1.9089404E-02 -1.4858169E-03 1,midg,midg; igrid,midg,midg -1.2600227E-02 1.2892333E-02 gauss-seidel spectral radius is 0.9982369 estimated iterations to convergence 189 setup time was (sec) 0.7300000 now iterating at: 19:12:04 rms-change max change #iterations 4.251005 141.8012 at 10iterations 1.792804 58.13073 at 20iterations 0.7609527 22.36739 at 30iterations 0.3238356 10.53073 at 40iterations 0.1386698 4.562338 at 50iterations 6.0596205E-02 1.825012 at 60iterations 2.8406668E-02 0.9647064 at 70iterations 1.5004687E-02 0.5315933 at 80iterations 9.1699315E-03 0.2978821 at 90iterations 6.3481908E-03 0.2055187 at 100iterations 4.6617975E-03 0.1480789 at 110iterations 3.4765699E-03 0.1100464 at 120iterations finished qdiffx linear iterations at : 19:12:12 total time elapsed so far: 7.980000 # loops : 120 mean,max change (kT/e) : 3.4765699E-03 0.1100464 energy calculations done at 7.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.120000 DelPhi exited at 19:12:12 8.122u 0.203s 0:08.60 96.7% 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 Sun Oct 9 2011 at 19:12:12 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 = 5129 !!! 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.358553 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): 3.341000 68.16000 ymin,ymax (A): -8.724000 59.19900 zmin,zma (A): -2.280000 62.00600 x,y,z range (A): 64.81900 67.92300 64.28600 scale (grids/A): 2.358553 object centre (A): 35.75050 25.23750 29.86300 number of atom coordinates read : 5129 total number of charged atoms : 4954 net assigned charge : 3.240037 assigned positive charge : 781.7942 centred at (gu) : 79.81158 81.65409 86.81399 assigned negative charge : -778.5596 centred at (gu) : 79.23352 81.72561 86.83305 start vw surface at 0.1300000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 241051 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40740 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 116958 mr = 182163 m= 33053 mr = 94547 m= 5321 mr = 24995 m= 319 mr = 3463 m= 6 mr = 141 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.250000 number of dielectric boundary points 91399 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 39 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 39530 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) : 1.572369 object centre at (A) : 35.75050 25.23750 29.86300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1613242 -0.2991475 midg,1,midg; midg,igrid,midg 0.1039809 -0.1084111 1,midg,midg; igrid,midg,midg -0.2469151 0.2120508 gauss-seidel spectral radius is 0.9991959 estimated iterations to convergence 278 setup time was (sec) 1.490000 now iterating at: 19:12:14 rms-change max change #iterations 11.25453 325.0436 at 10iterations 6.518947 150.1079 at 20iterations 3.747497 72.77251 at 30iterations 2.135579 41.71663 at 40iterations 1.216815 22.76057 at 50iterations 0.6915461 11.23374 at 60iterations 0.3912826 7.231258 at 70iterations 0.2218758 3.912182 at 80iterations 0.1256289 2.071281 at 90iterations 7.1337827E-02 1.358788 at 100iterations 4.0979337E-02 0.6970367 at 110iterations 2.3975659E-02 0.4425354 at 120iterations 1.4559016E-02 0.2744904 at 130iterations 9.3625328E-03 0.1884155 at 140iterations 6.4669000E-03 0.1268234 at 150iterations 4.8090359E-03 9.4444275E-02 at 160iterations 3.7650925E-03 7.5546265E-02 at 170iterations 3.0355460E-03 5.6755066E-02 at 180iterations finished qdiffx linear iterations at : 19:12:25 total time elapsed so far: 13.19000 # loops : 180 mean,max change (kT/e) : 3.0355460E-03 5.6755066E-02 energy calculations done at 13.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.32000 DelPhi exited at 19:12:26 13.326u 0.198s 0:13.80 97.8% 0+0k 0+0io 0pf+0w