Wed Feb 15 08:56:35 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:56:35 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 = 2388 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6219535 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): -2.835000 45.93200 ymin,ymax (A): -15.26600 29.61800 zmin,zma (A): -18.48800 38.75100 x,y,z range (A): 48.76700 44.88400 57.23900 scale (grids/A): 0.6219535 object centre (A): 21.54850 7.176000 10.13150 number of atom coordinates read : 2388 total number of charged atoms : 2255 net assigned charge : 3.000001 assigned positive charge : 345.8231 centred at (gu) : 90.19542 88.35288 89.61085 assigned negative charge : -342.8238 centred at (gu) : 90.22377 88.45016 89.66176 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6053 nv = 96 ne = 84 npr = 50952 no. pairs analyzed = 50952 no. exposed pairs = 2879 no. arc points = 19985 no. surface atoms = 987 nbur = 1401 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 289 mr = 3328 m= 0 mr = 36 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 2978 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2001 ## 191 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 7466 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.0719247E-09 -6.6329170E-10 midg,1,midg; midg,igrid,midg 1.2122825E-08 -2.5032147E-09 1,midg,midg; igrid,midg,midg 4.0164694E-09 6.9946793E-10 gauss-seidel spectral radius is 0.9865904 estimated iterations to convergence 71 setup time was (sec) 0.7100000 now iterating at: 08:56:36 rms-change max change #iterations 0.1185341 18.06540 at 10iterations 1.1157189E-02 2.076344 at 20iterations 1.0846353E-03 0.1590633 at 30iterations 1.2876556E-04 2.4915695E-02 at 40iterations 2.4633639E-05 4.9629211E-03 at 50iterations finished qdiffx linear iterations at : 08:56:40 total time elapsed so far: 4.960000 # loops : 50 mean,max change (kT/e) : 2.4633639E-05 4.9629211E-03 energy calculations done at 4.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.170000 DelPhi exited at 08:56:41 5.172u 0.449s 0:06.29 89.1% 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 Wed Feb 15 2012 at 08:56:41 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 = 2388 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.865861 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): -2.835000 45.93200 ymin,ymax (A): -15.26600 29.61800 zmin,zma (A): -18.48800 38.75100 x,y,z range (A): 48.76700 44.88400 57.23900 scale (grids/A): 1.865861 object centre (A): 21.54850 7.176000 10.13150 number of atom coordinates read : 2388 total number of charged atoms : 2255 net assigned charge : 3.000001 assigned positive charge : 345.8231 centred at (gu) : 90.58569 85.05785 88.83218 assigned negative charge : -342.8238 centred at (gu) : 90.67140 85.35017 88.98531 start vw surface at 0.1400000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 65538 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19985 grid for indexing accessible points = 1.400000 m= 22618 mr = 45558 m= 3465 mr = 16538 m= 181 mr = 2214 m= 4 mr = 72 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 249 time to turn everything in is 0.6500000 number of dielectric boundary points 27424 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 131 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 17702 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) : 0.6219535 object centre at (A) : 21.54850 7.176000 10.13150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0914877E-02 -4.8409807E-03 midg,1,midg; midg,igrid,midg 2.0446017E-02 -1.8853112E-03 1,midg,midg; igrid,midg,midg 3.2375692E-03 -2.9858854E-02 gauss-seidel spectral radius is 0.9985506 estimated iterations to convergence 208 setup time was (sec) 0.9800000 now iterating at: 08:56:43 rms-change max change #iterations 3.812844 183.7491 at 10iterations 1.737049 72.52016 at 20iterations 0.7956257 27.17369 at 30iterations 0.3651339 13.11457 at 40iterations 0.1666553 6.221937 at 50iterations 7.6500498E-02 2.579184 at 60iterations 3.4964174E-02 1.185978 at 70iterations 1.6039688E-02 0.5014267 at 80iterations 7.3534632E-03 0.2547121 at 90iterations 3.3803289E-03 0.1120720 at 100iterations 1.5510649E-03 5.3733826E-02 at 110iterations 7.1515661E-04 2.3393631E-02 at 120iterations finished qdiffx linear iterations at : 08:56:53 total time elapsed so far: 11.11000 # loops : 120 mean,max change (kT/e) : 7.1515661E-04 2.3393631E-02 energy calculations done at 11.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.33000 DelPhi exited at 08:56:54 11.337u 0.491s 0:12.50 94.5% 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 Wed Feb 15 2012 at 08:56:54 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 = 2388 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.798791 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): -2.835000 45.93200 ymin,ymax (A): -15.26600 29.61800 zmin,zma (A): -18.48800 38.75100 x,y,z range (A): 48.76700 44.88400 57.23900 scale (grids/A): 2.798791 object centre (A): 21.54850 7.176000 10.13150 number of atom coordinates read : 2388 total number of charged atoms : 2255 net assigned charge : 3.000001 assigned positive charge : 345.8231 centred at (gu) : 90.87838 82.58682 88.24825 assigned negative charge : -342.8238 centred at (gu) : 91.00710 83.02515 88.47796 start vw surface at 0.1400000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 151729 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19985 grid for indexing accessible points = 1.400000 m= 73876 mr = 110637 m= 26224 mr = 60191 m= 6362 mr = 21012 m= 803 mr = 4917 m= 45 mr = 516 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 818 time to turn everything in is 1.720000 number of dielectric boundary points 61746 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.890000 number of grid points assigned charge 18034 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) : 1.865861 object centre at (A) : 21.54850 7.176000 10.13150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2127959 -0.1454694 midg,1,midg; midg,igrid,midg 0.1722170 -4.6794463E-02 1,midg,midg; igrid,midg,midg 2.9054884E-02 -0.4619281 gauss-seidel spectral radius is 0.9992284 estimated iterations to convergence 284 setup time was (sec) 2.100000 now iterating at: 08:56:56 rms-change max change #iterations 9.070538 345.7043 at 10iterations 5.258723 125.8447 at 20iterations 3.019778 62.33186 at 30iterations 1.736545 34.11672 at 40iterations 0.9931493 19.50573 at 50iterations 0.5679407 12.10437 at 60iterations 0.3242101 6.364492 at 70iterations 0.1848296 3.907658 at 80iterations 0.1054024 1.983807 at 90iterations 6.0021628E-02 1.202011 at 100iterations 3.4139685E-02 0.6080418 at 110iterations 1.9428058E-02 0.3701386 at 120iterations 1.1064251E-02 0.2287521 at 130iterations 6.2992536E-03 0.1247644 at 140iterations 3.5945324E-03 7.0664406E-02 at 150iterations 2.0600855E-03 4.3277740E-02 at 160iterations 1.1855902E-03 2.3189545E-02 at 170iterations 6.8759336E-04 1.3927460E-02 at 180iterations finished qdiffx linear iterations at : 08:57:13 total time elapsed so far: 19.04000 # loops : 180 mean,max change (kT/e) : 6.8759336E-04 1.3927460E-02 energy calculations done at 19.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.25000 DelPhi exited at 08:57:14 19.252u 0.552s 0:20.21 97.9% 0+0k 0+0io 0pf+0w