Tue Oct 11 08:20:09 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 08:20:09 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3150 !!! WARNING: HIR 54 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5785607 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): 5.235000 48.56700 ymin,ymax (A): 78.37600 139.9080 zmin,zma (A): 103.0690 161.5590 x,y,z range (A): 43.33200 61.53201 58.49001 scale (grids/A): 0.5785607 object centre (A): 26.90100 109.1420 132.3140 number of atom coordinates read : 3150 total number of charged atoms : 3012 net assigned charge : -5.985970 assigned positive charge : 475.2538 centred at (gu) : 89.43507 91.98157 91.54095 assigned negative charge : -481.2409 centred at (gu) : 89.39139 91.98080 91.54762 start vw surface at 0.1900000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6778 nv = 96 ne = 84 npr = 65377 no. pairs analyzed = 65377 no. exposed pairs = 3936 no. arc points = 26772 no. surface atoms = 1333 nbur = 1817 mkacc time = 0.1400000 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 = 1.484000 m= 305 mr = 3568 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3485 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2809 ## 320 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 8794 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.6229328E-10 -1.9634772E-09 midg,1,midg; midg,igrid,midg -7.9653023E-10 -1.9050945E-09 1,midg,midg; igrid,midg,midg -2.5275255E-09 -2.2265101E-10 gauss-seidel spectral radius is 0.9845904 estimated iterations to convergence 66 setup time was (sec) 0.5700000 now iterating at: 08:20:10 rms-change max change #iterations 0.1067828 17.18217 at 10iterations 8.1055835E-03 1.285839 at 20iterations 8.0238667E-04 0.1347733 at 30iterations 1.8477226E-04 2.9345512E-02 at 40iterations 6.4379710E-05 1.0416985E-02 at 50iterations finished qdiffx linear iterations at : 08:20:12 total time elapsed so far: 3.000000 # loops : 50 mean,max change (kT/e) : 6.4379710E-05 1.0416985E-02 energy calculations done at 3.000000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.160000 DelPhi exited at 08:20:13 3.168u 0.138s 0:03.66 89.8% 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 08:20:13 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3150 !!! WARNING: HIR 54 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.735682 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): 5.235000 48.56700 ymin,ymax (A): 78.37600 139.9080 zmin,zma (A): 103.0690 161.5590 x,y,z range (A): 43.33200 61.53201 58.49001 scale (grids/A): 1.735682 object centre (A): 26.90100 109.1420 132.3140 number of atom coordinates read : 3150 total number of charged atoms : 3012 net assigned charge : -5.985970 assigned positive charge : 475.2538 centred at (gu) : 88.30430 95.94400 94.62202 assigned negative charge : -481.2409 centred at (gu) : 88.17363 95.94197 94.64264 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 73387 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26772 grid for indexing accessible points = 1.400000 m= 25279 mr = 50196 m= 3491 mr = 18082 m= 138 mr = 1981 m= 2 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 1590 time to turn everything in is 0.5100000 number of dielectric boundary points 32021 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 235 iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 23377 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) : 0.5785607 object centre at (A) : 26.90100 109.1420 132.3140 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2856728E-03 1.2308207E-02 midg,1,midg; midg,igrid,midg 2.5095176E-02 -1.6569924E-02 1,midg,midg; igrid,midg,midg -1.3112249E-02 -1.6392880E-03 gauss-seidel spectral radius is 0.9984078 estimated iterations to convergence 199 setup time was (sec) 0.7800000 now iterating at: 08:20:14 rms-change max change #iterations 3.967751 174.3067 at 10iterations 1.742248 58.64919 at 20iterations 0.7668971 24.99911 at 30iterations 0.3382263 11.53328 at 40iterations 0.1488616 4.947876 at 50iterations 6.5742314E-02 2.375242 at 60iterations 2.8975615E-02 0.9920540 at 70iterations 1.2815697E-02 0.4343805 at 80iterations 5.7029561E-03 0.1951408 at 90iterations 2.5715032E-03 8.2955360E-02 at 100iterations 1.1827458E-03 3.9979935E-02 at 110iterations 5.7544361E-04 2.1362305E-02 at 120iterations finished qdiffx linear iterations at : 08:20:20 total time elapsed so far: 6.940000 # loops : 120 mean,max change (kT/e) : 5.7544361E-04 2.1362305E-02 energy calculations done at 6.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.120000 DelPhi exited at 08:20:21 7.118u 0.167s 0:07.57 96.0% 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 08:20:21 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: 332 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3150 !!! WARNING: HIR 54 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.603523 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): 5.235000 48.56700 ymin,ymax (A): 78.37600 139.9080 zmin,zma (A): 103.0690 161.5590 x,y,z range (A): 43.33200 61.53201 58.49001 scale (grids/A): 2.603523 object centre (A): 26.90100 109.1420 132.3140 number of atom coordinates read : 3150 total number of charged atoms : 3012 net assigned charge : -5.985970 assigned positive charge : 475.2538 centred at (gu) : 87.45599 98.91563 96.93278 assigned negative charge : -481.2409 centred at (gu) : 87.26054 98.91286 96.96381 start vw surface at 0.1600000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 169912 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26772 grid for indexing accessible points = 1.400000 m= 83136 mr = 122032 m= 28354 mr = 67065 m= 5904 mr = 22096 m= 565 mr = 4209 m= 16 mr = 275 m= 0 mr = 3 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 5358 time to turn everything in is 1.240000 number of dielectric boundary points 72207 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 9 iepsmp to db, and charging done at 1.360000 number of grid points assigned charge 24079 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) : 1.735682 object centre at (A) : 26.90100 109.1420 132.3140 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1013511 0.4337517 midg,1,midg; midg,igrid,midg 0.6261794 -0.2752655 1,midg,midg; igrid,midg,midg -0.1518938 -1.9872259E-02 gauss-seidel spectral radius is 0.9992118 estimated iterations to convergence 281 setup time was (sec) 1.520000 now iterating at: 08:20:22 rms-change max change #iterations 9.906096 287.2750 at 10iterations 5.740460 132.8403 at 20iterations 3.288042 72.22220 at 30iterations 1.881921 40.15376 at 40iterations 1.074514 23.70779 at 50iterations 0.6102647 12.79064 at 60iterations 0.3464940 6.836851 at 70iterations 0.1960845 4.572735 at 80iterations 0.1112569 2.096924 at 90iterations 6.2992789E-02 1.200600 at 100iterations 3.5642076E-02 0.6781353 at 110iterations 2.0166054E-02 0.3742867 at 120iterations 1.1399786E-02 0.2316437 at 130iterations 6.4626671E-03 0.1346135 at 140iterations 3.6687909E-03 7.6858521E-02 at 150iterations 2.0870888E-03 4.1135788E-02 at 160iterations 1.2009967E-03 2.4360657E-02 at 170iterations 7.0262619E-04 1.3664246E-02 at 180iterations finished qdiffx linear iterations at : 08:20:32 total time elapsed so far: 11.17000 # loops : 180 mean,max change (kT/e) : 7.0262619E-04 1.3664246E-02 energy calculations done at 11.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.33000 DelPhi exited at 08:20:33 11.337u 0.199s 0:12.12 95.0% 0+0k 0+0io 0pf+0w