Tue Oct 11 07:52:17 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 Tue Oct 11 2011 at 07:52:17 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 = 2393 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: 0.6375472 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): -1.803000 54.03600 ymin,ymax (A): -22.77800 23.08700 zmin,zma (A): 9.098000 55.61000 x,y,z range (A): 55.83900 45.86500 46.51200 scale (grids/A): 0.6375472 object centre (A): 26.11650 0.1545000 32.35400 number of atom coordinates read : 2393 total number of charged atoms : 2257 net assigned charge : 6.500007 assigned positive charge : 359.9643 centred at (gu) : 88.67796 90.25855 89.72236 assigned negative charge : -353.4648 centred at (gu) : 88.70915 90.21363 89.51181 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 6640 nv = 96 ne = 84 npr = 47670 no. pairs analyzed = 47670 no. exposed pairs = 2953 no. arc points = 20833 no. surface atoms = 1002 nbur = 1391 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 341 mr = 3676 m= 3 mr = 50 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 0.2800000 number of dielectric boundary points 3258 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2062 ## 201 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 7841 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3358766E-08 2.7549204E-08 midg,1,midg; midg,igrid,midg 4.1423802E-09 1.4013698E-08 1,midg,midg; igrid,midg,midg 1.5772601E-08 4.4020441E-09 gauss-seidel spectral radius is 0.9872362 estimated iterations to convergence 72 setup time was (sec) 0.5400000 now iterating at: 07:52:18 rms-change max change #iterations 0.1387426 19.58024 at 10iterations 1.3517777E-02 1.997116 at 20iterations 1.4932249E-03 0.2374191 at 30iterations 1.9359677E-04 3.0433655E-02 at 40iterations 3.4600176E-05 5.1727295E-03 at 50iterations finished qdiffx linear iterations at : 07:52:22 total time elapsed so far: 4.220000 # loops : 50 mean,max change (kT/e) : 3.4600176E-05 5.1727295E-03 energy calculations done at 4.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.390000 DelPhi exited at 07:52:23 4.393u 0.413s 0:06.25 76.8% 0+0k 0+0io 6pf+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 07:52:23 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 = 2393 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.912642 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): -1.803000 54.03600 ymin,ymax (A): -22.77800 23.08700 zmin,zma (A): 9.098000 55.61000 x,y,z range (A): 55.83900 45.86500 46.51200 scale (grids/A): 1.912642 object centre (A): 26.11650 0.1545000 32.35400 number of atom coordinates read : 2393 total number of charged atoms : 2257 net assigned charge : 6.500007 assigned positive charge : 359.9643 centred at (gu) : 86.03343 90.77523 89.16669 assigned negative charge : -353.4648 centred at (gu) : 86.12741 90.64081 88.53518 start vw surface at 0.1100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 70739 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20833 grid for indexing accessible points = 1.400000 m= 26712 mr = 49287 m= 4130 mr = 19967 m= 230 mr = 2544 m= 5 mr = 84 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5700000 number of dielectric boundary points 29934 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 124 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 17728 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) : 0.6375472 object centre at (A) : 26.11650 0.1545000 32.35400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8157143E-02 4.4092815E-02 midg,1,midg; midg,igrid,midg -5.8694719E-04 5.5591348E-03 1,midg,midg; igrid,midg,midg 2.1796685E-02 2.7061300E-02 gauss-seidel spectral radius is 0.9986281 estimated iterations to convergence 214 setup time was (sec) 0.9000000 now iterating at: 07:52:25 rms-change max change #iterations 4.051073 177.3117 at 10iterations 1.891997 67.71773 at 20iterations 0.8913090 32.36647 at 30iterations 0.4162908 13.62493 at 40iterations 0.1959442 6.319599 at 50iterations 9.1382645E-02 2.839691 at 60iterations 4.2969283E-02 1.443209 at 70iterations 2.0108756E-02 0.7081223 at 80iterations 9.4541227E-03 0.2876492 at 90iterations 4.4594966E-03 0.1433983 at 100iterations 2.1068524E-03 6.8983078E-02 at 110iterations 1.0070715E-03 3.4803391E-02 at 120iterations finished qdiffx linear iterations at : 07:52:34 total time elapsed so far: 10.43000 # loops : 120 mean,max change (kT/e) : 1.0070715E-03 3.4803391E-02 energy calculations done at 10.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.59000 DelPhi exited at 07:52:35 10.597u 0.454s 0:11.35 97.2% 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 07:52:35 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 = 2393 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.868962 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): -1.803000 54.03600 ymin,ymax (A): -22.77800 23.08700 zmin,zma (A): 9.098000 55.61000 x,y,z range (A): 55.83900 45.86500 46.51200 scale (grids/A): 2.868962 object centre (A): 26.11650 0.1545000 32.35400 number of atom coordinates read : 2393 total number of charged atoms : 2257 net assigned charge : 6.500007 assigned positive charge : 359.9643 centred at (gu) : 84.05000 91.16280 88.74991 assigned negative charge : -353.4648 centred at (gu) : 84.19109 90.96111 87.80273 start vw surface at 0.1300000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 163252 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20833 grid for indexing accessible points = 1.400000 m= 85699 mr = 118951 m= 31656 mr = 70975 m= 7171 mr = 25551 m= 967 mr = 5273 m= 55 mr = 660 m= 0 mr = 27 time to grow re-entrant surface = 0.9400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.550000 number of dielectric boundary points 67363 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.680000 number of grid points assigned charge 18052 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) : 1.912642 object centre at (A) : 26.11650 0.1545000 32.35400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2601031 0.4502402 midg,1,midg; midg,igrid,midg -7.9685599E-03 -2.7375171E-02 1,midg,midg; igrid,midg,midg 0.1075998 0.1861879 gauss-seidel spectral radius is 0.9992507 estimated iterations to convergence 288 setup time was (sec) 1.870000 now iterating at: 07:52:37 rms-change max change #iterations 9.511961 383.7209 at 10iterations 5.551984 127.6480 at 20iterations 3.222536 69.61537 at 30iterations 1.861842 43.97215 at 40iterations 1.076988 22.72094 at 50iterations 0.6194309 13.41173 at 60iterations 0.3570799 7.573252 at 70iterations 0.2050145 3.623608 at 80iterations 0.1176911 2.251740 at 90iterations 6.7578532E-02 1.194082 at 100iterations 3.8773730E-02 0.7328500 at 110iterations 2.2242090E-02 0.4217162 at 120iterations 1.2718182E-02 0.2661285 at 130iterations 7.2972360E-03 0.1408920 at 140iterations 4.1915532E-03 7.8660011E-02 at 150iterations 2.4093792E-03 4.5299530E-02 at 160iterations 1.3854735E-03 2.7225494E-02 at 170iterations 7.9764717E-04 1.5851974E-02 at 180iterations finished qdiffx linear iterations at : 07:52:53 total time elapsed so far: 17.40000 # loops : 180 mean,max change (kT/e) : 7.9764717E-04 1.5851974E-02 energy calculations done at 17.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.57000 DelPhi exited at 07:52:53 17.577u 0.455s 0:18.32 98.3% 0+0k 0+0io 0pf+0w