Sun Oct 9 18:56:55 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 18:56:55 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5254 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 0.5473217 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): 3.256000 68.30000 ymin,ymax (A): -9.065000 53.33900 zmin,zma (A): -0.9680000 63.47300 x,y,z range (A): 65.04401 62.40400 64.44100 scale (grids/A): 0.5473217 object centre (A): 35.77800 22.13700 31.25250 number of atom coordinates read : 5254 total number of charged atoms : 5106 net assigned charge : -0.3789444 assigned positive charge : 807.1841 centred at (gu) : 88.19019 89.20433 89.07248 assigned negative charge : -807.5695 centred at (gu) : 88.05733 89.24694 89.02105 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 10274 nv = 96 ne = 84 npr = 106432 no. pairs analyzed = 106432 no. exposed pairs = 6112 no. arc points = 41977 no. surface atoms = 2082 nbur = 3172 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 = 1.568000 m= 441 mr = 5853 m= 2 mr = 29 m= 0 mr = 0 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 4835 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4226 ## 486 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 13485 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.0914137E-10 5.2080040E-10 midg,1,midg; midg,igrid,midg 6.6886163E-10 -4.3270756E-10 1,midg,midg; igrid,midg,midg -2.6786895E-09 1.0588432E-09 gauss-seidel spectral radius is 0.9829529 estimated iterations to convergence 63 setup time was (sec) 0.5300000 now iterating at: 18:56:56 rms-change max change #iterations 0.1031050 14.49185 at 10iterations 9.0794051E-03 1.511547 at 20iterations 2.5516294E-03 0.2888870 at 30iterations 1.1279326E-03 0.1441379 at 40iterations 5.2099465E-04 7.2149754E-02 at 50iterations finished qdiffx linear iterations at : 18:56:59 total time elapsed so far: 3.460000 # loops : 50 mean,max change (kT/e) : 5.2099465E-04 7.2149754E-02 energy calculations done at 3.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.600000 DelPhi exited at 18:56:59 3.605u 0.183s 0:04.07 92.8% 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 18:56:59 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5254 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 1.641965 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): 3.256000 68.30000 ymin,ymax (A): -9.065000 53.33900 zmin,zma (A): -0.9680000 63.47300 x,y,z range (A): 65.04401 62.40400 64.44100 scale (grids/A): 1.641965 object centre (A): 35.77800 22.13700 31.25250 number of atom coordinates read : 5254 total number of charged atoms : 5106 net assigned charge : -0.3789444 assigned positive charge : 807.1841 centred at (gu) : 84.56910 87.61154 87.21593 assigned negative charge : -807.5695 centred at (gu) : 84.17142 87.74069 87.06335 start vw surface at 0.1300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 114920 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41977 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 39483 mr = 83312 m= 4629 mr = 28548 m= 135 mr = 2458 m= 2 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 84 time to turn everything in is 0.5500000 number of dielectric boundary points 44837 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 396 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 39099 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) : 0.5473217 object centre at (A) : 35.77800 22.13700 31.25250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.9114610E-02 -6.2551904E-03 midg,1,midg; midg,igrid,midg 2.1226224E-02 7.9809595E-03 1,midg,midg; igrid,midg,midg -2.8924366E-02 8.1700506E-03 gauss-seidel spectral radius is 0.9984113 estimated iterations to convergence 199 setup time was (sec) 0.7800000 now iterating at: 18:57:00 rms-change max change #iterations 4.809115 157.6242 at 10iterations 2.118695 66.92619 at 20iterations 0.9377625 25.26447 at 30iterations 0.4151033 11.00848 at 40iterations 0.1832717 5.194071 at 50iterations 8.1517257E-02 2.280136 at 60iterations 3.6645133E-02 1.044485 at 70iterations 1.6770478E-02 0.4818115 at 80iterations 8.1387311E-03 0.2661171 at 90iterations 4.3621268E-03 0.1248589 at 100iterations 2.6810700E-03 8.1970215E-02 at 110iterations 1.8414395E-03 5.2688599E-02 at 120iterations finished qdiffx linear iterations at : 18:57:08 total time elapsed so far: 8.070000 # loops : 120 mean,max change (kT/e) : 1.8414395E-03 5.2688599E-02 energy calculations done at 8.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.210000 DelPhi exited at 18:57:08 8.210u 0.197s 0:08.77 95.7% 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 18:57:08 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5254 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 2.462948 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): 3.256000 68.30000 ymin,ymax (A): -9.065000 53.33900 zmin,zma (A): -0.9680000 63.47300 x,y,z range (A): 65.04401 62.40400 64.44100 scale (grids/A): 2.462948 object centre (A): 35.77800 22.13700 31.25250 number of atom coordinates read : 5254 total number of charged atoms : 5106 net assigned charge : -0.3789444 assigned positive charge : 807.1841 centred at (gu) : 81.85316 86.41694 85.82349 assigned negative charge : -807.5695 centred at (gu) : 81.25713 86.61107 85.59492 start vw surface at 0.1400000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 267080 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41977 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 133692 mr = 202551 m= 41753 mr = 109063 m= 7528 mr = 32446 m= 601 mr = 5172 m= 11 mr = 298 m= 0 mr = 0 time to grow re-entrant surface = 0.8300000 no. cavity mid-points inaccessible to solvent = 223 time to turn everything in is 1.430000 number of dielectric boundary points 101135 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 32 iepsmp to db, and charging done at 1.530000 number of grid points assigned charge 40793 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) : 1.641965 object centre at (A) : 35.77800 22.13700 31.25250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4608750 -0.1917658 midg,1,midg; midg,igrid,midg 0.2189762 -7.6536634E-03 1,midg,midg; igrid,midg,midg -0.5292307 7.5005010E-02 gauss-seidel spectral radius is 0.9992498 estimated iterations to convergence 288 setup time was (sec) 1.670000 now iterating at: 18:57:10 rms-change max change #iterations 12.22958 388.0669 at 10iterations 7.191952 163.7541 at 20iterations 4.209040 75.06667 at 30iterations 2.450525 45.33966 at 40iterations 1.423548 23.60917 at 50iterations 0.8228272 14.17139 at 60iterations 0.4754404 7.837311 at 70iterations 0.2741257 4.445879 at 80iterations 0.1575624 2.458451 at 90iterations 9.1073416E-02 1.561668 at 100iterations 5.2575625E-02 0.8484192 at 110iterations 3.0447450E-02 0.4862323 at 120iterations 1.7769618E-02 0.2978249 at 130iterations 1.0627449E-02 0.1933060 at 140iterations 6.5302989E-03 0.1163840 at 150iterations 4.2336332E-03 7.6780319E-02 at 160iterations 2.9448962E-03 5.6579590E-02 at 170iterations 2.1906060E-03 4.2360306E-02 at 180iterations finished qdiffx linear iterations at : 18:57:22 total time elapsed so far: 13.58000 # loops : 180 mean,max change (kT/e) : 2.1906060E-03 4.2360306E-02 energy calculations done at 13.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.72000 DelPhi exited at 18:57:23 13.720u 0.226s 0:14.22 98.0% 0+0k 0+0io 0pf+0w