Mon Oct 10 14:00:18 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 Mon Oct 10 2011 at 14:00:18 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 = 2339 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: 0.6552550 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): -0.2530000 54.07700 ymin,ymax (A): 8.046000 49.82500 zmin,zma (A): -12.43500 39.45300 x,y,z range (A): 54.33000 41.77900 51.88800 scale (grids/A): 0.6552550 object centre (A): 26.91200 28.93550 13.50900 number of atom coordinates read : 2339 total number of charged atoms : 2204 net assigned charge : 14.00002 assigned positive charge : 342.4123 centred at (gu) : 89.66150 90.86980 91.55793 assigned negative charge : -328.4131 centred at (gu) : 89.65092 90.87591 91.53385 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 6755 nv = 96 ne = 84 npr = 47265 no. pairs analyzed = 47265 no. exposed pairs = 3015 no. arc points = 21472 no. surface atoms = 1007 nbur = 1332 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 415 mr = 3557 m= 1 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 61 time to turn everything in is 0.2700000 number of dielectric boundary points 3568 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2068 ## 192 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7949 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0226999E-08 4.7719528E-08 midg,1,midg; midg,igrid,midg 2.6884750E-08 3.6045133E-08 1,midg,midg; igrid,midg,midg 3.1648739E-08 3.0524742E-08 gauss-seidel spectral radius is 0.9879114 estimated iterations to convergence 74 setup time was (sec) 0.5500000 now iterating at: 14:00:19 rms-change max change #iterations 0.1450613 23.46961 at 10iterations 1.5432918E-02 2.154335 at 20iterations 1.6490462E-03 0.2503548 at 30iterations 2.2834948E-04 3.6490440E-02 at 40iterations 5.7163987E-05 1.2152672E-02 at 50iterations finished qdiffx linear iterations at : 14:00:22 total time elapsed so far: 3.990000 # loops : 50 mean,max change (kT/e) : 5.7163987E-05 1.2152672E-02 energy calculations done at 3.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.170000 DelPhi exited at 14:00:23 4.178u 0.212s 0:04.98 87.9% 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 Mon Oct 10 2011 at 14:00:23 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 = 2339 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: 1.965765 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): -0.2530000 54.07700 ymin,ymax (A): 8.046000 49.82500 zmin,zma (A): -12.43500 39.45300 x,y,z range (A): 54.33000 41.77900 51.88800 scale (grids/A): 1.965765 object centre (A): 26.91200 28.93550 13.50900 number of atom coordinates read : 2339 total number of charged atoms : 2204 net assigned charge : 14.00002 assigned positive charge : 342.4123 centred at (gu) : 88.98426 92.60910 94.67339 assigned negative charge : -328.4131 centred at (gu) : 88.95273 92.62769 94.60159 start vw surface at 0.1700000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 72248 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21472 grid for indexing accessible points = 1.400000 m= 25999 mr = 48595 m= 4560 mr = 18789 m= 314 mr = 2882 m= 4 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 1952 time to turn everything in is 0.6600000 number of dielectric boundary points 32734 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 126 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 17400 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) : 0.6552550 object centre at (A) : 26.91200 28.93550 13.50900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9553744E-02 3.4458488E-02 midg,1,midg; midg,igrid,midg 1.3780889E-02 3.2922737E-02 1,midg,midg; igrid,midg,midg 5.3495392E-02 5.2302800E-02 gauss-seidel spectral radius is 0.9986953 estimated iterations to convergence 219 setup time was (sec) 1.000000 now iterating at: 14:00:24 rms-change max change #iterations 4.088982 177.1169 at 10iterations 1.945960 73.26139 at 20iterations 0.9269451 35.31927 at 30iterations 0.4401589 16.75461 at 40iterations 0.2101606 6.579137 at 50iterations 9.9967189E-02 3.074619 at 60iterations 4.7348462E-02 1.606448 at 70iterations 2.2583142E-02 0.6977639 at 80iterations 1.0766094E-02 0.3681335 at 90iterations 5.1563717E-03 0.1646309 at 100iterations 2.4744750E-03 7.7864885E-02 at 110iterations 1.1936310E-03 3.5296202E-02 at 120iterations finished qdiffx linear iterations at : 14:00:33 total time elapsed so far: 9.490000 # loops : 120 mean,max change (kT/e) : 1.1936310E-03 3.5296202E-02 energy calculations done at 9.490000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.650000 DelPhi exited at 14:00:34 9.657u 0.298s 0:10.77 92.2% 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 Mon Oct 10 2011 at 14:00:34 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 = 2339 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: 2.948647 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): -0.2530000 54.07700 ymin,ymax (A): 8.046000 49.82500 zmin,zma (A): -12.43500 39.45300 x,y,z range (A): 54.33000 41.77900 51.88800 scale (grids/A): 2.948647 object centre (A): 26.91200 28.93550 13.50900 number of atom coordinates read : 2339 total number of charged atoms : 2204 net assigned charge : 14.00002 assigned positive charge : 342.4123 centred at (gu) : 88.47638 93.91360 97.00996 assigned negative charge : -328.4131 centred at (gu) : 88.42903 93.94169 96.90240 start vw surface at 0.1800000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 166922 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21472 grid for indexing accessible points = 1.400000 m= 83079 mr = 118377 m= 31173 mr = 66851 m= 8346 mr = 24783 m= 1395 mr = 6288 m= 82 mr = 952 m= 2 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 6918 time to turn everything in is 1.560000 number of dielectric boundary points 73705 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.700000 number of grid points assigned charge 17631 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) : 1.965765 object centre at (A) : 26.91200 28.93550 13.50900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6739825 0.3638372 midg,1,midg; midg,igrid,midg 9.1629528E-02 0.3036759 1,midg,midg; igrid,midg,midg 0.5520781 0.4902814 gauss-seidel spectral radius is 0.9992781 estimated iterations to convergence 294 setup time was (sec) 1.900000 now iterating at: 14:00:36 rms-change max change #iterations 9.676883 416.9672 at 10iterations 5.727425 139.2559 at 20iterations 3.365980 72.20718 at 30iterations 1.979071 41.99693 at 40iterations 1.155321 23.38666 at 50iterations 0.6742107 13.18824 at 60iterations 0.3934532 7.506998 at 70iterations 0.2285516 4.599709 at 80iterations 0.1332017 2.663568 at 90iterations 7.7323243E-02 1.415706 at 100iterations 4.4900101E-02 0.7999840 at 110iterations 2.6089201E-02 0.5095863 at 120iterations 1.5122516E-02 0.2776505 at 130iterations 8.7895840E-03 0.1698399 at 140iterations 5.1148543E-03 9.9143982E-02 at 150iterations 2.9816332E-03 5.5534363E-02 at 160iterations 1.7525139E-03 3.3237457E-02 at 170iterations 1.0412934E-03 2.4257660E-02 at 180iterations finished qdiffx linear iterations at : 14:00:50 total time elapsed so far: 15.27000 # loops : 180 mean,max change (kT/e) : 1.0412934E-03 2.4257660E-02 energy calculations done at 15.27000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.45000 DelPhi exited at 14:00:50 15.453u 0.266s 0:16.43 95.6% 0+0k 0+0io 0pf+0w