Sat Oct 15 15:27:29 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 15 2011 at 15:27:29 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2743 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6641915 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): -12.35400 37.01600 ymin,ymax (A): -25.88500 22.44400 zmin,zma (A): -8.235000 45.36400 x,y,z range (A): 49.37000 48.32900 53.59900 scale (grids/A): 0.6641915 object centre (A): 12.33100 -1.720500 18.56450 number of atom coordinates read : 2743 total number of charged atoms : 2591 net assigned charge : 2.176013 assigned positive charge : 417.4778 centred at (gu) : 90.35567 90.33337 91.32629 assigned negative charge : -415.3023 centred at (gu) : 90.09509 90.15685 91.23527 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8063 nv = 96 ne = 84 npr = 56404 no. pairs analyzed = 56404 no. exposed pairs = 3316 no. arc points = 22812 no. surface atoms = 1111 nbur = 1632 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 458 mr = 4627 m= 3 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 32 time to turn everything in is 0.2100000 number of dielectric boundary points 3837 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2283 ## 233 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9617 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2059613E-08 3.5432517E-08 midg,1,midg; midg,igrid,midg -3.4200781E-08 4.9732485E-08 1,midg,midg; igrid,midg,midg -5.3256048E-08 7.0329961E-08 gauss-seidel spectral radius is 0.9882587 estimated iterations to convergence 75 setup time was (sec) 0.4200000 now iterating at: 15:27:30 rms-change max change #iterations 0.1770820 23.54410 at 10iterations 1.9909179E-02 2.869026 at 20iterations 2.3297493E-03 0.3822784 at 30iterations 3.6144184E-04 5.5835724E-02 at 40iterations 8.8492918E-05 1.0829926E-02 at 50iterations finished qdiffx linear iterations at : 15:27:33 total time elapsed so far: 3.550000 # loops : 50 mean,max change (kT/e) : 8.8492918E-05 1.0829926E-02 energy calculations done at 3.550000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.690000 DelPhi exited at 15:27:33 3.699u 0.210s 0:04.22 92.4% 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 15 2011 at 15:27:33 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2743 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.992574 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): -12.35400 37.01600 ymin,ymax (A): -25.88500 22.44400 zmin,zma (A): -8.235000 45.36400 x,y,z range (A): 49.37000 48.32900 53.59900 scale (grids/A): 1.992574 object centre (A): 12.33100 -1.720500 18.56450 number of atom coordinates read : 2743 total number of charged atoms : 2591 net assigned charge : 2.176013 assigned positive charge : 417.4778 centred at (gu) : 91.06682 90.99979 93.97826 assigned negative charge : -415.3023 centred at (gu) : 90.28520 90.47013 93.70568 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 86522 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22812 grid for indexing accessible points = 1.400000 m= 32931 mr = 61484 m= 5494 mr = 24877 m= 366 mr = 3530 m= 5 mr = 165 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1276 time to turn everything in is 0.4300000 number of dielectric boundary points 35262 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 143 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 20503 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) : 0.6641915 object centre at (A) : 12.33100 -1.720500 18.56450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.1966535E-02 2.2535578E-03 midg,1,midg; midg,igrid,midg -1.3842735E-02 3.6800057E-02 1,midg,midg; igrid,midg,midg -1.0293215E-02 8.8112384E-02 gauss-seidel spectral radius is 0.9987592 estimated iterations to convergence 225 setup time was (sec) 0.6700000 now iterating at: 15:27:34 rms-change max change #iterations 4.840595 221.2085 at 10iterations 2.355203 79.56752 at 20iterations 1.140011 42.13586 at 30iterations 0.5545852 16.77814 at 40iterations 0.2709641 8.100565 at 50iterations 0.1314947 3.799171 at 60iterations 6.3900925E-02 1.994961 at 70iterations 3.1170014E-02 0.8699980 at 80iterations 1.5237074E-02 0.4622498 at 90iterations 7.4333847E-03 0.2055533 at 100iterations 3.6728627E-03 0.1034851 at 110iterations 1.8217301E-03 5.6560516E-02 at 120iterations finished qdiffx linear iterations at : 15:27:47 total time elapsed so far: 8.180000 # loops : 120 mean,max change (kT/e) : 1.8217301E-03 5.6560516E-02 energy calculations done at 8.180000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.310000 DelPhi exited at 15:27:48 8.312u 0.230s 0:14.17 60.2% 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 Sat Oct 15 2011 at 15:27:48 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2743 !!! WARNING: HIR 70 has a net charge of 0.5140 !!! WARNING: TYS 1 has a net charge of -0.3380 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.988862 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): -12.35400 37.01600 ymin,ymax (A): -25.88500 22.44400 zmin,zma (A): -8.235000 45.36400 x,y,z range (A): 49.37000 48.32900 53.59900 scale (grids/A): 2.988862 object centre (A): 12.33100 -1.720500 18.56450 number of atom coordinates read : 2743 total number of charged atoms : 2591 net assigned charge : 2.176013 assigned positive charge : 417.4778 centred at (gu) : 91.59992 91.49967 95.96728 assigned negative charge : -415.3023 centred at (gu) : 90.42772 90.70506 95.55848 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 200023 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22812 grid for indexing accessible points = 1.400000 m= 105292 mr = 148600 m= 39810 mr = 87384 m= 10013 mr = 32608 m= 1474 mr = 7554 m= 134 mr = 998 m= 4 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 0.6899999 no. cavity mid-points inaccessible to solvent = 4536 time to turn everything in is 1.190000 number of dielectric boundary points 79520 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 20718 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) : 1.992574 object centre at (A) : 12.33100 -1.720500 18.56450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6506106 0.2101530 midg,1,midg; midg,igrid,midg -0.1392986 0.4203445 1,midg,midg; igrid,midg,midg -8.1274994E-02 0.7600991 gauss-seidel spectral radius is 0.9992887 estimated iterations to convergence 296 setup time was (sec) 1.460000 now iterating at: 15:27:49 rms-change max change #iterations 11.08721 426.1088 at 10iterations 6.520290 144.8428 at 20iterations 3.833199 74.24310 at 30iterations 2.254035 46.40014 at 40iterations 1.320789 28.86618 at 50iterations 0.7729716 15.88386 at 60iterations 0.4525267 7.790678 at 70iterations 0.2643299 4.831743 at 80iterations 0.1545482 2.647631 at 90iterations 8.9905754E-02 1.464599 at 100iterations 5.2566636E-02 0.9257126 at 110iterations 3.0708479E-02 0.5188980 at 120iterations 1.7978495E-02 0.3008194 at 130iterations 1.0542392E-02 0.1799469 at 140iterations 6.2215067E-03 0.1124420 at 150iterations 3.7253399E-03 6.2804222E-02 at 160iterations 2.2709910E-03 4.0161133E-02 at 170iterations 1.4254071E-03 2.5741577E-02 at 180iterations finished qdiffx linear iterations at : 15:28:01 total time elapsed so far: 13.70000 # loops : 180 mean,max change (kT/e) : 1.4254071E-03 2.5741577E-02 energy calculations done at 13.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.83000 DelPhi exited at 15:28:02 13.828u 0.269s 0:14.46 97.3% 0+0k 0+0io 0pf+0w