Tue Oct 11 06:31:37 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 06:31:37 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 = 1994 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: 0.7342931 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): -20.32700 24.69300 ymin,ymax (A): -28.57800 11.02400 zmin,zma (A): -11.72700 36.75500 x,y,z range (A): 45.02000 39.60200 48.48200 scale (grids/A): 0.7342931 object centre (A): 2.183001 -8.777000 12.51400 number of atom coordinates read : 1994 total number of charged atoms : 1888 net assigned charge : 6.500006 assigned positive charge : 304.5301 centred at (gu) : 89.98511 90.55116 88.97064 assigned negative charge : -298.0302 centred at (gu) : 89.80453 90.51017 88.88866 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7368 nv = 96 ne = 84 npr = 39716 no. pairs analyzed = 39716 no. exposed pairs = 2399 no. arc points = 16462 no. surface atoms = 813 nbur = 1181 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 572 mr = 4329 m= 7 mr = 114 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 3504 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1547 ## 161 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 8028 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.8057060E-08 1.4068796E-07 midg,1,midg; midg,igrid,midg 6.1084393E-08 1.5079139E-07 1,midg,midg; igrid,midg,midg -5.2754892E-08 2.5028757E-07 gauss-seidel spectral radius is 0.9903176 estimated iterations to convergence 83 setup time was (sec) 0.4900000 now iterating at: 06:31:38 rms-change max change #iterations 0.2255541 33.27985 at 10iterations 3.0537136E-02 4.011597 at 20iterations 4.1155731E-03 0.4932556 at 30iterations 5.8304105E-04 7.6007605E-02 at 40iterations 9.8499018E-05 1.1365891E-02 at 50iterations finished qdiffx linear iterations at : 06:31:42 total time elapsed so far: 4.290000 # loops : 50 mean,max change (kT/e) : 9.8499018E-05 1.1365891E-02 energy calculations done at 4.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.470000 DelPhi exited at 06:31:43 4.472u 0.397s 0:05.34 91.0% 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 06:31:43 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 = 1994 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: 2.202879 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): -20.32700 24.69300 ymin,ymax (A): -28.57800 11.02400 zmin,zma (A): -11.72700 36.75500 x,y,z range (A): 45.02000 39.60200 48.48200 scale (grids/A): 2.202879 object centre (A): 2.183001 -8.777000 12.51400 number of atom coordinates read : 1994 total number of charged atoms : 1888 net assigned charge : 6.500006 assigned positive charge : 304.5301 centred at (gu) : 89.95537 91.65353 86.91207 assigned negative charge : -298.0302 centred at (gu) : 89.41365 91.53069 86.66621 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 77814 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16462 grid for indexing accessible points = 1.400000 m= 32127 mr = 55644 m= 6803 mr = 24658 m= 729 mr = 4632 m= 24 mr = 395 m= 0 mr = 7 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6900000 number of dielectric boundary points 32161 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 47 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 15026 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) : 0.7342931 object centre at (A) : 2.183001 -8.777000 12.51400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.8673720E-02 4.9223341E-02 midg,1,midg; midg,igrid,midg 4.4184700E-03 4.2962570E-02 1,midg,midg; igrid,midg,midg 3.1042090E-02 5.6826249E-02 gauss-seidel spectral radius is 0.9988949 estimated iterations to convergence 238 setup time was (sec) 1.020000 now iterating at: 06:31:44 rms-change max change #iterations 4.774893 206.5031 at 10iterations 2.412193 81.59557 at 20iterations 1.222445 36.40478 at 30iterations 0.6216058 18.13686 at 40iterations 0.3131187 9.054541 at 50iterations 0.1592052 4.444021 at 60iterations 8.0479689E-02 2.671406 at 70iterations 4.0869527E-02 1.185364 at 80iterations 2.0729804E-02 0.6299133 at 90iterations 1.0496566E-02 0.3183289 at 100iterations 5.3527816E-03 0.1563854 at 110iterations 2.7287987E-03 7.9111099E-02 at 120iterations finished qdiffx linear iterations at : 06:31:54 total time elapsed so far: 10.79000 # loops : 120 mean,max change (kT/e) : 2.7287987E-03 7.9111099E-02 energy calculations done at 10.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.96000 DelPhi exited at 06:31:55 10.964u 0.446s 0:12.05 94.6% 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 Tue Oct 11 2011 at 06:31:55 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 = 1994 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: 3.304319 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): -20.32700 24.69300 ymin,ymax (A): -28.57800 11.02400 zmin,zma (A): -11.72700 36.75500 x,y,z range (A): 45.02000 39.60200 48.48200 scale (grids/A): 3.304319 object centre (A): 2.183001 -8.777000 12.51400 number of atom coordinates read : 1994 total number of charged atoms : 1888 net assigned charge : 6.500006 assigned positive charge : 304.5301 centred at (gu) : 89.93299 92.48028 85.36806 assigned negative charge : -298.0302 centred at (gu) : 89.12053 92.29610 84.99945 start vw surface at 0.1000000 fill in re-entrant regions at 0.8000000 boundary points on vw surface= 179479 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16462 grid for indexing accessible points = 1.400000 m= 99087 mr = 133745 m= 41842 mr = 82886 m= 12947 mr = 34788 m= 2744 mr = 10087 m= 388 mr = 2013 m= 23 mr = 271 m= 0 mr = 11 time to grow re-entrant surface = 1.110000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.040000 number of dielectric boundary points 72709 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.190000 number of grid points assigned charge 15104 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) : 2.202879 object centre at (A) : 2.183001 -8.777000 12.51400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3150274 0.3787398 midg,1,midg; midg,igrid,midg 1.4247903E-02 0.3260681 1,midg,midg; igrid,midg,midg 0.4192811 0.4131396 gauss-seidel spectral radius is 0.9993079 estimated iterations to convergence 300 setup time was (sec) 2.380000 now iterating at: 06:31:58 rms-change max change #iterations 10.47189 299.3744 at 10iterations 6.222260 127.6794 at 20iterations 3.685361 76.10459 at 30iterations 2.187094 39.33952 at 40iterations 1.293641 22.77090 at 50iterations 0.7623484 12.65978 at 60iterations 0.4484679 8.166748 at 70iterations 0.2638336 4.905893 at 80iterations 0.1557247 2.538177 at 90iterations 9.1496281E-02 1.630880 at 100iterations 5.3875688E-02 0.8433733 at 110iterations 3.1793244E-02 0.5545807 at 120iterations 1.8840417E-02 0.3375435 at 130iterations 1.1212219E-02 0.2070694 at 140iterations 6.7949938E-03 0.1292715 at 150iterations 4.2130486E-03 7.2307587E-02 at 160iterations 2.7062837E-03 4.7378540E-02 at 170iterations 1.8392638E-03 3.2855988E-02 at 180iterations finished qdiffx linear iterations at : 06:32:15 total time elapsed so far: 19.25000 # loops : 180 mean,max change (kT/e) : 1.8392638E-03 3.2855988E-02 energy calculations done at 19.25000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.42000 DelPhi exited at 06:32:16 19.420u 0.474s 0:21.17 93.9% 0+0k 0+0io 0pf+0w