Sat Oct 8 17:25:40 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 Sat Oct 8 2011 at 17:25:40 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3765 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5548714 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): -1.860000 60.16200 ymin,ymax (A): -18.42000 44.54800 zmin,zma (A): -5.338000 58.82100 x,y,z range (A): 62.02200 62.96800 64.15900 scale (grids/A): 0.5548714 object centre (A): 29.15100 13.06400 26.74150 number of atom coordinates read : 3765 total number of charged atoms : 3614 net assigned charge : -8.999962 assigned positive charge : 573.3762 centred at (gu) : 88.86657 86.78635 90.58311 assigned negative charge : -582.3789 centred at (gu) : 88.94939 86.78690 90.59420 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7629 nv = 96 ne = 84 npr = 75679 no. pairs analyzed = 75679 no. exposed pairs = 4931 no. arc points = 34540 no. surface atoms = 1635 nbur = 2130 mkacc time = 0.1300000 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 = 1.540000 m= 320 mr = 3921 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 4012 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3476 ## 448 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 9916 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.7396243E-10 -1.0589916E-09 midg,1,midg; midg,igrid,midg -1.6979268E-09 -3.7734452E-10 1,midg,midg; igrid,midg,midg 2.5986369E-10 -1.3572953E-09 gauss-seidel spectral radius is 0.9833124 estimated iterations to convergence 64 setup time was (sec) 0.4600000 now iterating at: 17:25:41 rms-change max change #iterations 9.1944106E-02 15.17151 at 10iterations 6.5536140E-03 0.9899697 at 20iterations 5.8525265E-04 8.9914322E-02 at 30iterations 1.1182113E-04 1.9062042E-02 at 40iterations 3.1571028E-05 5.2442551E-03 at 50iterations finished qdiffx linear iterations at : 17:25:43 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 3.1571028E-05 5.2442551E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 17:25:44 3.437u 0.162s 0:03.87 92.7% 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 Sat Oct 8 2011 at 17:25:44 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3765 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.664614 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): -1.860000 60.16200 ymin,ymax (A): -18.42000 44.54800 zmin,zma (A): -5.338000 58.82100 x,y,z range (A): 62.02200 62.96800 64.15900 scale (grids/A): 1.664614 object centre (A): 29.15100 13.06400 26.74150 number of atom coordinates read : 3765 total number of charged atoms : 3614 net assigned charge : -8.999962 assigned positive charge : 573.3762 centred at (gu) : 86.59860 80.35797 91.74827 assigned negative charge : -582.3789 centred at (gu) : 86.84782 80.36036 91.78241 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 84357 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34540 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 26568 mr = 57418 m= 2891 mr = 17913 m= 77 mr = 1342 m= 3 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 28 time to turn everything in is 0.4200000 number of dielectric boundary points 37219 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 390 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 27818 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) : 0.5548714 object centre at (A) : 29.15100 13.06400 26.74150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1944239E-03 -6.2187668E-03 midg,1,midg; midg,igrid,midg -2.8472517E-02 -8.9838142E-03 1,midg,midg; igrid,midg,midg -1.0747600E-02 -3.5967827E-02 gauss-seidel spectral radius is 0.9983312 estimated iterations to convergence 194 setup time was (sec) 0.6500000 now iterating at: 17:25:45 rms-change max change #iterations 4.015172 164.6476 at 10iterations 1.727770 67.80688 at 20iterations 0.7487397 23.64777 at 30iterations 0.3231609 9.982605 at 40iterations 0.1396422 4.369087 at 50iterations 6.0321219E-02 2.113380 at 60iterations 2.6049612E-02 0.8598270 at 70iterations 1.1314516E-02 0.3413391 at 80iterations 4.9163229E-03 0.1618080 at 90iterations 2.1364426E-03 7.2109222E-02 at 100iterations 9.4174588E-04 3.2295763E-02 at 110iterations 4.2193863E-04 1.4488220E-02 at 120iterations finished qdiffx linear iterations at : 17:25:52 total time elapsed so far: 7.700000 # loops : 120 mean,max change (kT/e) : 4.2193863E-04 1.4488220E-02 energy calculations done at 7.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.830000 DelPhi exited at 17:25:52 7.828u 0.179s 0:08.27 96.6% 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 Sat Oct 8 2011 at 17:25:52 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3765 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.496922 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): -1.860000 60.16200 ymin,ymax (A): -18.42000 44.54800 zmin,zma (A): -5.338000 58.82100 x,y,z range (A): 62.02200 62.96800 64.15900 scale (grids/A): 2.496922 object centre (A): 29.15100 13.06400 26.74150 number of atom coordinates read : 3765 total number of charged atoms : 3614 net assigned charge : -8.999962 assigned positive charge : 573.3762 centred at (gu) : 84.89759 75.53663 92.62196 assigned negative charge : -582.3789 centred at (gu) : 85.27170 75.54047 92.67361 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 195895 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34540 grid for indexing accessible points = 1.400000 m= 91668 mr = 140444 m= 26307 mr = 72198 m= 4392 mr = 19272 m= 315 mr = 2709 m= 6 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 103 time to turn everything in is 1.010000 number of dielectric boundary points 83872 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 1.110000 number of grid points assigned charge 28885 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) : 1.664614 object centre at (A) : 29.15100 13.06400 26.74150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1736659E-02 0.1033654 midg,1,midg; midg,igrid,midg -0.4272154 -0.1049765 1,midg,midg; igrid,midg,midg -0.1769619 -0.6427507 gauss-seidel spectral radius is 0.9992001 estimated iterations to convergence 279 setup time was (sec) 1.250000 now iterating at: 17:25:54 rms-change max change #iterations 10.33603 302.4127 at 10iterations 5.941039 137.6887 at 20iterations 3.394682 80.74845 at 30iterations 1.934641 46.37759 at 40iterations 1.097790 20.64481 at 50iterations 0.6221408 12.43862 at 60iterations 0.3513741 6.953710 at 70iterations 0.1986866 3.823624 at 80iterations 0.1117303 2.012972 at 90iterations 6.2978275E-02 1.109965 at 100iterations 3.5467550E-02 0.6988857 at 110iterations 1.9977935E-02 0.3754396 at 120iterations 1.1241822E-02 0.2314272 at 130iterations 6.3353158E-03 0.1244469 at 140iterations 3.5688190E-03 6.6282749E-02 at 150iterations 2.0185977E-03 3.7311077E-02 at 160iterations 1.1457560E-03 2.3529053E-02 at 170iterations 6.5299275E-04 1.2473106E-02 at 180iterations finished qdiffx linear iterations at : 17:26:05 total time elapsed so far: 12.76000 # loops : 180 mean,max change (kT/e) : 6.5299275E-04 1.2473106E-02 energy calculations done at 12.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.89000 DelPhi exited at 17:26:06 12.895u 0.214s 0:13.38 97.9% 0+0k 0+0io 0pf+0w