Mon Oct 10 16:11:22 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 Mon Oct 10 2011 at 16:11:22 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4381 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: 0.5504530 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): 7.366000 59.01300 ymin,ymax (A): -29.64700 34.24300 zmin,zma (A): -29.15700 35.51700 x,y,z range (A): 51.64700 63.89000 64.67400 scale (grids/A): 0.5504530 object centre (A): 33.18950 2.298000 3.180001 number of atom coordinates read : 4381 total number of charged atoms : 4226 net assigned charge : 5.000016 assigned positive charge : 652.7908 centred at (gu) : 90.04113 89.56647 88.47997 assigned negative charge : -647.7944 centred at (gu) : 90.01575 89.54172 88.45402 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8665 nv = 96 ne = 84 npr = 89401 no. pairs analyzed = 89401 no. exposed pairs = 5261 no. arc points = 35853 no. surface atoms = 1772 nbur = 2609 mkacc time = 0.3000000 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 = 1.568000 m= 343 mr = 4820 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.3499999 no. cavity mid-points inaccessible to solvent = 11 time to turn everything in is 0.5900000 number of dielectric boundary points 4172 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3635 ## 431 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 11311 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0584947E-10 4.6463342E-10 midg,1,midg; midg,igrid,midg 1.0106201E-10 5.9129279E-10 1,midg,midg; igrid,midg,midg 8.4586650E-11 6.7078421E-10 gauss-seidel spectral radius is 0.9830840 estimated iterations to convergence 63 setup time was (sec) 0.9200000 now iterating at: 16:11:23 rms-change max change #iterations 9.4398849E-02 12.45527 at 10iterations 6.9209519E-03 0.9523735 at 20iterations 1.1252357E-03 0.1919365 at 30iterations 4.2634225E-04 6.1901093E-02 at 40iterations 1.8070512E-04 2.4806976E-02 at 50iterations finished qdiffx linear iterations at : 16:11:27 total time elapsed so far: 4.510000 # loops : 50 mean,max change (kT/e) : 1.8070512E-04 2.4806976E-02 energy calculations done at 4.510000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.740000 DelPhi exited at 16:11:28 4.749u 0.450s 0:05.47 94.8% 0+0k 0+0io 5pf+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 Mon Oct 10 2011 at 16:11:28 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4381 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: 1.651359 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): 7.366000 59.01300 ymin,ymax (A): -29.64700 34.24300 zmin,zma (A): -29.15700 35.51700 x,y,z range (A): 51.64700 63.89000 64.67400 scale (grids/A): 1.651359 object centre (A): 33.18950 2.298000 3.180001 number of atom coordinates read : 4381 total number of charged atoms : 4226 net assigned charge : 5.000016 assigned positive charge : 652.7908 centred at (gu) : 90.12209 88.69791 85.43868 assigned negative charge : -647.7944 centred at (gu) : 90.04705 88.62471 85.36186 start vw surface at 0.2000000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 96612 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35853 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 31595 mr = 68985 m= 3434 mr = 22325 m= 88 mr = 1807 m= 0 mr = 4 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 391 time to turn everything in is 0.9600000 number of dielectric boundary points 38608 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 393 ## 4 charges are in solution ## iepsmp to db, and charging done at 1.100000 number of grid points assigned charge 32452 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) : 0.5504530 object centre at (A) : 33.18950 2.298000 3.180001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.0046476E-02 -1.9524336E-03 midg,1,midg; midg,igrid,midg 1.3826153E-02 1.0342554E-02 1,midg,midg; igrid,midg,midg 2.5012691E-03 -1.3215269E-04 gauss-seidel spectral radius is 0.9983655 estimated iterations to convergence 196 setup time was (sec) 1.300000 now iterating at: 16:11:29 rms-change max change #iterations 4.216130 163.4361 at 10iterations 1.837890 56.07587 at 20iterations 0.8027484 24.56506 at 30iterations 0.3506620 10.73687 at 40iterations 0.1535547 4.505336 at 50iterations 6.7042202E-02 1.947959 at 60iterations 2.9579856E-02 0.8473759 at 70iterations 1.3052404E-02 0.3916149 at 80iterations 5.8643003E-03 0.1929722 at 90iterations 2.7739883E-03 8.6049080E-02 at 100iterations 1.4330301E-03 4.4320464E-02 at 110iterations 8.4448332E-04 2.5733948E-02 at 120iterations finished qdiffx linear iterations at : 16:11:39 total time elapsed so far: 10.58000 # loops : 120 mean,max change (kT/e) : 8.4448332E-04 2.5733948E-02 energy calculations done at 10.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.80000 DelPhi exited at 16:11:39 10.808u 0.473s 0:11.56 97.4% 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 Mon Oct 10 2011 at 16:11:39 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4381 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: 2.477039 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): 7.366000 59.01300 ymin,ymax (A): -29.64700 34.24300 zmin,zma (A): -29.15700 35.51700 x,y,z range (A): 51.64700 63.89000 64.67400 scale (grids/A): 2.477039 object centre (A): 33.18950 2.298000 3.180001 number of atom coordinates read : 4381 total number of charged atoms : 4226 net assigned charge : 5.000016 assigned positive charge : 652.7908 centred at (gu) : 90.18288 88.04639 83.15775 assigned negative charge : -647.7944 centred at (gu) : 90.07025 87.93697 83.04272 start vw surface at 0.2200000 fill in re-entrant regions at 0.7900000 boundary points on vw surface= 224934 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35853 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 108360 mr = 168671 m= 31980 mr = 86978 m= 5601 mr = 24555 m= 448 mr = 3863 m= 13 mr = 210 m= 0 mr = 0 time to grow re-entrant surface = 1.510000 no. cavity mid-points inaccessible to solvent = 1445 time to turn everything in is 2.460000 number of dielectric boundary points 87059 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 2.630000 number of grid points assigned charge 33775 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) : 1.651359 object centre at (A) : 33.18950 2.298000 3.180001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3744505 -9.2214145E-02 midg,1,midg; midg,igrid,midg 0.3110009 0.1097387 1,midg,midg; igrid,midg,midg 3.3563312E-02 -7.9532631E-04 gauss-seidel spectral radius is 0.9992243 estimated iterations to convergence 283 setup time was (sec) 2.830000 now iterating at: 16:11:42 rms-change max change #iterations 10.85543 347.8719 at 10iterations 6.332252 125.5450 at 20iterations 3.671083 74.62806 at 30iterations 2.120684 44.21267 at 40iterations 1.221742 24.47051 at 50iterations 0.7029278 13.16170 at 60iterations 0.4019808 7.861711 at 70iterations 0.2305056 4.594285 at 80iterations 0.1317165 2.395608 at 90iterations 7.5180061E-02 1.290260 at 100iterations 4.2902868E-02 0.8079300 at 110iterations 2.4534253E-02 0.4092712 at 120iterations 1.4063042E-02 0.2325573 at 130iterations 8.1012994E-03 0.1382523 at 140iterations 4.7215498E-03 7.9163551E-02 at 150iterations 2.8166196E-03 5.3228378E-02 at 160iterations 1.7436803E-03 3.1185150E-02 at 170iterations 1.1456334E-03 2.2518158E-02 at 180iterations finished qdiffx linear iterations at : 16:11:58 total time elapsed so far: 18.60000 # loops : 180 mean,max change (kT/e) : 1.1456334E-03 2.2518158E-02 energy calculations done at 18.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.82000 DelPhi exited at 16:11:59 18.822u 0.467s 0:19.58 98.4% 0+0k 0+0io 0pf+0w