Tue Oct 11 03:35:47 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 03:35:48 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2273 !!! WARNING: ASP 461 has a net charge of -0.2720 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: 0.5547073 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): -27.61800 36.56000 ymin,ymax (A): -7.195000 41.56100 zmin,zma (A): 4.869000 51.40300 x,y,z range (A): 64.17799 48.75600 46.53400 scale (grids/A): 0.5547073 object centre (A): 4.470999 17.18300 28.13600 number of atom coordinates read : 2273 total number of charged atoms : 2188 net assigned charge : -5.771980 assigned positive charge : 337.4432 centred at (gu) : 92.02299 89.96757 89.88607 assigned negative charge : -343.2157 centred at (gu) : 92.05755 90.04006 89.77888 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 4612 nv = 96 ne = 84 npr = 45615 no. pairs analyzed = 45615 no. exposed pairs = 2989 no. arc points = 21409 no. surface atoms = 999 nbur = 1274 mkacc time = 9.9999994E-02 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 = 1.540000 m= 190 mr = 2262 m= 0 mr = 10 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 2530 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2160 ## 242 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 5987 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2939935E-09 2.4321761E-10 midg,1,midg; midg,igrid,midg 1.2261722E-11 -1.0008605E-09 1,midg,midg; igrid,midg,midg -1.6033386E-10 -1.2074679E-09 gauss-seidel spectral radius is 0.9831871 estimated iterations to convergence 63 setup time was (sec) 0.5500000 now iterating at: 03:35:48 rms-change max change #iterations 6.9928713E-02 13.36193 at 10iterations 4.7362670E-03 0.8546963 at 20iterations 3.2079007E-04 5.2511215E-02 at 30iterations 2.3113871E-05 4.1046143E-03 at 40iterations 1.5882523E-06 2.6226044E-04 at 50iterations finished qdiffx linear iterations at : 03:35:51 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 1.5882523E-06 2.6226044E-04 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 03:35:51 3.389u 0.156s 0:03.90 90.5% 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 03:35:51 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 = 2273 !!! WARNING: ASP 461 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.664122 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): -27.61800 36.56000 ymin,ymax (A): -7.195000 41.56100 zmin,zma (A): 4.869000 51.40300 x,y,z range (A): 64.17799 48.75600 46.53400 scale (grids/A): 1.664122 object centre (A): 4.470999 17.18300 28.13600 number of atom coordinates read : 2273 total number of charged atoms : 2188 net assigned charge : -5.771980 assigned positive charge : 337.4432 centred at (gu) : 96.06873 89.90228 89.65776 assigned negative charge : -343.2157 centred at (gu) : 96.17243 90.12018 89.33648 start vw surface at 0.1700000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 50617 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21409 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 14576 mr = 33028 m= 1520 mr = 9666 m= 33 mr = 707 m= 0 mr = 4 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 57 time to turn everything in is 0.4200000 number of dielectric boundary points 23341 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 218 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 16866 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) : 0.5547073 object centre at (A) : 4.470999 17.18300 28.13600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.2220361E-03 7.8217788E-03 midg,1,midg; midg,igrid,midg 2.7691750E-03 -8.6882152E-03 1,midg,midg; igrid,midg,midg -2.4167327E-03 -2.5726765E-02 gauss-seidel spectral radius is 0.9981787 estimated iterations to convergence 186 setup time was (sec) 0.7000000 now iterating at: 03:35:52 rms-change max change #iterations 2.955112 140.9870 at 10iterations 1.223184 53.70057 at 20iterations 0.5096453 22.94696 at 30iterations 0.2124885 8.292131 at 40iterations 8.7670982E-02 3.547130 at 50iterations 3.6522988E-02 1.542695 at 60iterations 1.5169523E-02 0.6191593 at 70iterations 6.2912432E-03 0.2619009 at 80iterations 2.6185135E-03 0.1093483 at 90iterations 1.0920527E-03 4.4260025E-02 at 100iterations 4.5394580E-04 1.7349243E-02 at 110iterations 1.8920738E-04 7.9574585E-03 at 120iterations finished qdiffx linear iterations at : 03:35:59 total time elapsed so far: 7.210000 # loops : 120 mean,max change (kT/e) : 1.8920738E-04 7.9574585E-03 energy calculations done at 7.210000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.410000 DelPhi exited at 03:36:00 7.408u 0.171s 0:08.26 91.6% 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 03:36:00 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 = 2273 !!! WARNING: ASP 461 has a net charge of -0.2720 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: 2.496183 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): -27.61800 36.56000 ymin,ymax (A): -7.195000 41.56100 zmin,zma (A): 4.869000 51.40300 x,y,z range (A): 64.17799 48.75600 46.53400 scale (grids/A): 2.496183 object centre (A): 4.470999 17.18300 28.13600 number of atom coordinates read : 2273 total number of charged atoms : 2188 net assigned charge : -5.771980 assigned positive charge : 337.4432 centred at (gu) : 99.10308 89.85326 89.48640 assigned negative charge : -343.2157 centred at (gu) : 99.25850 90.18025 89.00475 start vw surface at 0.1900000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 117777 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21409 grid for indexing accessible points = 1.400000 m= 50671 mr = 81447 m= 14191 mr = 39129 m= 2230 mr = 10331 m= 123 mr = 1462 m= 3 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 231 time to turn everything in is 0.9900000 number of dielectric boundary points 52582 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 17482 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) : 1.664122 object centre at (A) : 4.470999 17.18300 28.13600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.6125091E-02 0.1715854 midg,1,midg; midg,igrid,midg 3.6496557E-02 -0.1074895 1,midg,midg; igrid,midg,midg -0.1078068 -0.3423119 gauss-seidel spectral radius is 0.9991177 estimated iterations to convergence 266 setup time was (sec) 1.290000 now iterating at: 03:36:01 rms-change max change #iterations 7.570596 287.8653 at 10iterations 4.172826 111.8475 at 20iterations 2.292742 59.27067 at 30iterations 1.255449 28.41168 at 40iterations 0.6861666 18.93291 at 50iterations 0.3754106 8.528486 at 60iterations 0.2043689 4.626177 at 70iterations 0.1113128 2.425150 at 80iterations 6.0512546E-02 1.418957 at 90iterations 3.3009928E-02 0.7472630 at 100iterations 1.7958136E-02 0.4305115 at 110iterations 9.7648101E-03 0.2204103 at 120iterations 5.3093564E-03 0.1217899 at 130iterations 2.8924542E-03 6.5225601E-02 at 140iterations 1.5730597E-03 4.1419983E-02 at 150iterations 8.5442147E-04 2.1274567E-02 at 160iterations 4.6405345E-04 1.0375977E-02 at 170iterations 2.5310970E-04 5.2757263E-03 at 180iterations finished qdiffx linear iterations at : 03:36:11 total time elapsed so far: 11.38000 # loops : 180 mean,max change (kT/e) : 2.5310970E-04 5.2757263E-03 energy calculations done at 11.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.56000 DelPhi exited at 03:36:12 11.565u 0.194s 0:12.32 95.3% 0+0k 0+0io 0pf+0w