Tue Oct 11 03:15:50 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+sph2.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 = amb2.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 Tue Oct 11 2011 at 03:15:50 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: 372 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5085 !!! WARNING: HIR 53 has a net charge of 0.5140 !!! WARNING: HIR 299 has a net charge of 0.5140 !!! WARNING: HIQ 351 has a net charge of 0.5140 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: 0.4919913 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): 16.07700 85.50900 ymin,ymax (A): 4.961000 68.35500 zmin,zma (A): 2.060000 74.41900 x,y,z range (A): 69.43201 63.39400 72.35900 scale (grids/A): 0.4919913 object centre (A): 50.79300 36.65800 38.23950 number of atom coordinates read : 5085 total number of charged atoms : 4797 net assigned charge : 1.542014 assigned positive charge : 762.7343 centred at (gu) : 91.64339 90.88734 91.49115 assigned negative charge : -761.1982 centred at (gu) : 91.67757 90.80298 91.44389 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7724 nv = 96 ne = 84 npr = 102313 no. pairs analyzed = 102313 no. exposed pairs = 6367 no. arc points = 44951 no. surface atoms = 2117 nbur = 2968 mkacc time = 0.2600000 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 = 1.708000 m= 255 mr = 4004 m= 0 mr = 2 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 77 time to turn everything in is 0.5100000 number of dielectric boundary points 3973 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3983 ## 608 charges are in solution ## iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 10246 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.2550036E-11 9.7508342E-11 midg,1,midg; midg,igrid,midg -7.4008077E-11 1.3844823E-10 1,midg,midg; igrid,midg,midg 3.1276967E-11 -5.2954311E-11 gauss-seidel spectral radius is 0.9789066 estimated iterations to convergence 57 setup time was (sec) 0.8000000 now iterating at: 03:15:51 rms-change max change #iterations 6.1968844E-02 11.38449 at 10iterations 3.1635850E-03 0.4826355 at 20iterations 2.6972295E-04 3.7858963E-02 at 30iterations 6.1639723E-05 8.3554983E-03 at 40iterations 1.7013388E-05 2.3617744E-03 at 50iterations finished qdiffx linear iterations at : 03:15:55 total time elapsed so far: 5.030000 # loops : 50 mean,max change (kT/e) : 1.7013388E-05 2.3617744E-03 energy calculations done at 5.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.190000 DelPhi exited at 03:15:56 5.197u 0.429s 0:06.01 93.3% 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 Tue Oct 11 2011 at 03:15:56 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: 372 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5085 !!! WARNING: HIR 53 has a net charge of 0.5140 !!! WARNING: HIR 299 has a net charge of 0.5140 !!! WARNING: HIQ 351 has a net charge of 0.5140 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: 1.475974 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): 16.07700 85.50900 ymin,ymax (A): 4.961000 68.35500 zmin,zma (A): 2.060000 74.41900 x,y,z range (A): 69.43201 63.39400 72.35900 scale (grids/A): 1.475974 object centre (A): 50.79300 36.65800 38.23950 number of atom coordinates read : 5085 total number of charged atoms : 4797 net assigned charge : 1.542014 assigned positive charge : 762.7343 centred at (gu) : 94.92850 92.66050 94.47142 assigned negative charge : -761.1982 centred at (gu) : 95.03218 92.40865 94.33127 start vw surface at 0.1900000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 87591 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44951 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 24559 mr = 59385 m= 1872 mr = 16591 m= 38 mr = 719 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 4822 time to turn everything in is 0.7400000 number of dielectric boundary points 37365 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 479 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 35576 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) : 0.4919913 object centre at (A) : 50.79300 36.65800 38.23950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3161362E-03 1.3472974E-02 midg,1,midg; midg,igrid,midg -5.4482454E-03 -1.4904430E-03 1,midg,midg; igrid,midg,midg 2.6031863E-03 -5.8882511E-03 gauss-seidel spectral radius is 0.9979797 estimated iterations to convergence 177 setup time was (sec) 1.040000 now iterating at: 03:15:57 rms-change max change #iterations 3.626916 186.9706 at 10iterations 1.435060 55.26816 at 20iterations 0.5716189 20.52857 at 30iterations 0.2273279 7.809135 at 40iterations 9.0306744E-02 3.095020 at 50iterations 3.6088333E-02 1.093495 at 60iterations 1.4332885E-02 0.5267992 at 70iterations 5.7149483E-03 0.1892910 at 80iterations 2.2960852E-03 7.7484131E-02 at 90iterations 9.3074003E-04 2.9405594E-02 at 100iterations 3.9075458E-04 1.3584495E-02 at 110iterations 1.7412435E-04 6.3219070E-03 at 120iterations finished qdiffx linear iterations at : 03:16:09 total time elapsed so far: 12.13000 # loops : 120 mean,max change (kT/e) : 1.7412435E-04 6.3219070E-03 energy calculations done at 12.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.30000 DelPhi exited at 03:16:09 12.308u 0.457s 0:13.25 96.2% 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 Tue Oct 11 2011 at 03:16:09 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: 372 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5085 !!! WARNING: HIR 53 has a net charge of 0.5140 !!! WARNING: HIR 299 has a net charge of 0.5140 !!! WARNING: HIQ 351 has a net charge of 0.5140 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: 2.213961 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): 16.07700 85.50900 ymin,ymax (A): 4.961000 68.35500 zmin,zma (A): 2.060000 74.41900 x,y,z range (A): 69.43201 63.39400 72.35900 scale (grids/A): 2.213961 object centre (A): 50.79300 36.65800 38.23950 number of atom coordinates read : 5085 total number of charged atoms : 4797 net assigned charge : 1.542014 assigned positive charge : 762.7343 centred at (gu) : 97.39229 93.99040 96.70670 assigned negative charge : -761.1982 centred at (gu) : 97.54807 93.61292 96.49684 start vw surface at 0.1800000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 204260 reading accessible surface arcs data from file ARCDAT no. of arc points read = 44951 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 89099 mr = 145889 m= 21512 mr = 70105 m= 2565 mr = 15736 m= 75 mr = 1442 m= 0 mr = 10 time to grow re-entrant surface = 1.070000 no. cavity mid-points inaccessible to solvent = 16538 time to turn everything in is 1.760000 number of dielectric boundary points 84329 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 83 iepsmp to db, and charging done at 1.910000 number of grid points assigned charge 38229 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) : 1.475974 object centre at (A) : 50.79300 36.65800 38.23950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.6365309E-02 0.1401735 midg,1,midg; midg,igrid,midg -3.7928548E-02 -5.9708308E-02 1,midg,midg; igrid,midg,midg 2.8099500E-02 -0.1662068 gauss-seidel spectral radius is 0.9991254 estimated iterations to convergence 267 setup time was (sec) 2.110000 now iterating at: 03:16:12 rms-change max change #iterations 9.951716 279.0287 at 10iterations 5.579196 136.6988 at 20iterations 3.124028 66.46784 at 30iterations 1.738477 44.48833 at 40iterations 0.9642568 24.86176 at 50iterations 0.5334813 9.816607 at 60iterations 0.2949988 6.111472 at 70iterations 0.1626372 3.393547 at 80iterations 8.9619018E-02 1.857670 at 90iterations 4.9390621E-02 0.9918194 at 100iterations 2.7180122E-02 0.5411358 at 110iterations 1.4939428E-02 0.2957458 at 120iterations 8.1918631E-03 0.1631627 at 130iterations 4.5176847E-03 9.2128754E-02 at 140iterations 2.4825665E-03 5.0127029E-02 at 150iterations 1.3674413E-03 2.6565552E-02 at 160iterations 7.5826416E-04 1.4875412E-02 at 170iterations 4.2391024E-04 8.1286430E-03 at 180iterations finished qdiffx linear iterations at : 03:16:30 total time elapsed so far: 20.19000 # loops : 180 mean,max change (kT/e) : 4.2391024E-04 8.1286430E-03 energy calculations done at 20.19000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.37000 DelPhi exited at 03:16:31 20.372u 0.450s 0:21.24 98.0% 0+0k 0+0io 0pf+0w