Sat Oct 15 13:40:13 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 13:40:16 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2750 !!! WARNING: HIT 235 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5779034 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): 111.6270 173.2290 ymin,ymax (A): -41.43600 7.302000 zmin,zma (A): 50.29300 104.8670 x,y,z range (A): 61.60199 48.73800 54.57400 scale (grids/A): 0.5779034 object centre (A): 142.4280 -17.06700 77.58000 number of atom coordinates read : 2750 total number of charged atoms : 2607 net assigned charge : 16.01400 assigned positive charge : 405.3590 centred at (gu) : 90.23280 88.43633 88.83893 assigned negative charge : -389.3456 centred at (gu) : 90.15704 88.36940 88.67097 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6203 nv = 96 ne = 84 npr = 52051 no. pairs analyzed = 52051 no. exposed pairs = 4253 no. arc points = 31454 no. surface atoms = 1404 nbur = 1346 mkacc time = 0.1200000 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= 335 mr = 2581 m= 3 mr = 17 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 0.2700000 number of dielectric boundary points 3943 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3148 ## 394 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7870 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.4758412E-10 4.7739404E-09 midg,1,midg; midg,igrid,midg 2.9641374E-09 3.1388780E-09 1,midg,midg; igrid,midg,midg 1.8350612E-09 4.8996478E-09 gauss-seidel spectral radius is 0.9845506 estimated iterations to convergence 66 setup time was (sec) 0.5200000 now iterating at: 13:40:20 rms-change max change #iterations 9.1693617E-02 17.56821 at 10iterations 6.7956676E-03 1.166092 at 20iterations 5.3931843E-04 8.6823463E-02 at 30iterations 4.9407776E-05 7.5960159E-03 at 40iterations 6.8914151E-06 7.8964233E-04 at 50iterations finished qdiffx linear iterations at : 13:40:31 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 6.8914151E-06 7.8964233E-04 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 13:40:35 3.477u 0.213s 0:19.18 19.1% 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 13:40:37 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2750 !!! WARNING: HIT 235 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.733710 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): 111.6270 173.2290 ymin,ymax (A): -41.43600 7.302000 zmin,zma (A): 50.29300 104.8670 x,y,z range (A): 61.60199 48.73800 54.57400 scale (grids/A): 1.733710 object centre (A): 142.4280 -17.06700 77.58000 number of atom coordinates read : 2750 total number of charged atoms : 2607 net assigned charge : 16.01400 assigned positive charge : 405.3590 centred at (gu) : 90.69794 85.30888 86.51619 assigned negative charge : -389.3456 centred at (gu) : 90.47079 85.10796 86.01276 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 65802 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31454 grid for indexing accessible points = 1.400000 m= 20540 mr = 38532 m= 2775 mr = 12928 m= 111 mr = 1269 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.4500000 number of dielectric boundary points 36491 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 288 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 20234 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) : 0.5779034 object centre at (A) : 142.4280 -17.06700 77.58000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.5067214E-04 2.5744069E-02 midg,1,midg; midg,igrid,midg 2.1852909E-02 1.3145285E-02 1,midg,midg; igrid,midg,midg 1.3350272E-02 3.3328481E-02 gauss-seidel spectral radius is 0.9984044 estimated iterations to convergence 199 setup time was (sec) 0.7100000 now iterating at: 13:40:43 rms-change max change #iterations 3.549473 171.7678 at 10iterations 1.559872 60.60345 at 20iterations 0.6815876 27.30675 at 30iterations 0.2992067 11.32628 at 40iterations 0.1311853 5.004875 at 50iterations 5.7287939E-02 1.939301 at 60iterations 2.5215644E-02 0.8604174 at 70iterations 1.1067852E-02 0.3827258 at 80iterations 4.8604920E-03 0.1811543 at 90iterations 2.1399159E-03 8.6665869E-02 at 100iterations 9.3899429E-04 3.8139343E-02 at 110iterations 4.1380225E-04 1.4542937E-02 at 120iterations finished qdiffx linear iterations at : 13:41:04 total time elapsed so far: 7.160000 # loops : 120 mean,max change (kT/e) : 4.1380225E-04 1.4542937E-02 energy calculations done at 7.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.330000 DelPhi exited at 13:41:06 7.328u 0.161s 0:29.37 25.4% 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 13:41:09 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: 258 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2750 !!! WARNING: HIT 235 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.600565 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): 111.6270 173.2290 ymin,ymax (A): -41.43600 7.302000 zmin,zma (A): 50.29300 104.8670 x,y,z range (A): 61.60199 48.73800 54.57400 scale (grids/A): 2.600565 object centre (A): 142.4280 -17.06700 77.58000 number of atom coordinates read : 2750 total number of charged atoms : 2607 net assigned charge : 16.01400 assigned positive charge : 405.3590 centred at (gu) : 91.04683 82.96318 84.77418 assigned negative charge : -389.3456 centred at (gu) : 90.70616 82.66198 84.01912 start vw surface at 0.1300000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 151749 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31454 grid for indexing accessible points = 1.400000 m= 66831 mr = 95434 m= 22493 mr = 49259 m= 4573 mr = 16076 m= 417 mr = 2785 m= 12 mr = 161 m= 0 mr = 0 time to grow re-entrant surface = 0.6899999 no. cavity mid-points inaccessible to solvent = 54 time to turn everything in is 1.170000 number of dielectric boundary points 82360 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 7 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 20844 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) : 1.733710 object centre at (A) : 142.4280 -17.06700 77.58000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.7532796E-02 0.3538516 midg,1,midg; midg,igrid,midg 0.2748776 0.1300253 1,midg,midg; igrid,midg,midg 0.1272507 0.2503318 gauss-seidel spectral radius is 0.9992242 estimated iterations to convergence 283 setup time was (sec) 1.480000 now iterating at: 13:41:13 rms-change max change #iterations 9.070527 274.4365 at 10iterations 5.337850 137.1805 at 20iterations 3.097847 90.85646 at 30iterations 1.788096 46.47389 at 40iterations 1.029856 28.62779 at 50iterations 0.5879758 14.42589 at 60iterations 0.3350698 8.575310 at 70iterations 0.1914527 4.667866 at 80iterations 0.1089872 2.413927 at 90iterations 6.2030137E-02 1.328301 at 100iterations 3.5235126E-02 0.7725060 at 110iterations 2.0001886E-02 0.4320116 at 120iterations 1.1366842E-02 0.2526598 at 130iterations 6.4498694E-03 0.1440506 at 140iterations 3.6459551E-03 8.3414078E-02 at 150iterations 2.0709618E-03 4.1107178E-02 at 160iterations 1.1724815E-03 2.5085449E-02 at 170iterations 6.6448015E-04 1.3050079E-02 at 180iterations finished qdiffx linear iterations at : 13:41:46 total time elapsed so far: 12.47000 # loops : 180 mean,max change (kT/e) : 6.6448015E-04 1.3050079E-02 energy calculations done at 12.47000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.63000 DelPhi exited at 13:41:50 12.637u 0.243s 0:41.96 30.6% 0+0k 0+0io 0pf+0w