Mon Oct 10 14:00:47 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 Mon Oct 10 2011 at 14:00:47 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 = 2724 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 0.5726788 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): -20.79700 41.36700 ymin,ymax (A): -12.62900 44.53300 zmin,zma (A): -1.779000 52.49800 x,y,z range (A): 62.16399 57.16200 54.27700 scale (grids/A): 0.5726788 object centre (A): 10.28500 15.95200 25.35950 number of atom coordinates read : 2724 total number of charged atoms : 2578 net assigned charge : 11.00002 assigned positive charge : 397.8381 centred at (gu) : 91.72324 91.15611 86.63215 assigned negative charge : -386.8386 centred at (gu) : 91.85996 91.23884 86.39456 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6018 nv = 96 ne = 84 npr = 52713 no. pairs analyzed = 52713 no. exposed pairs = 4074 no. arc points = 29873 no. surface atoms = 1359 nbur = 1365 mkacc time = 0.1100000 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= 298 mr = 2611 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3698 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2939 ## 348 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7617 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.7629562E-09 2.4689952E-09 midg,1,midg; midg,igrid,midg 2.4557285E-09 1.0148604E-09 1,midg,midg; igrid,midg,midg 2.6657532E-09 -8.7971852E-11 gauss-seidel spectral radius is 0.9842628 estimated iterations to convergence 66 setup time was (sec) 0.5500000 now iterating at: 14:00:48 rms-change max change #iterations 8.6885408E-02 14.07574 at 10iterations 6.5059047E-03 1.104824 at 20iterations 4.9356755E-04 7.4308395E-02 at 30iterations 4.4905173E-05 6.3810349E-03 at 40iterations 6.3026177E-06 7.0381165E-04 at 50iterations finished qdiffx linear iterations at : 14:00:51 total time elapsed so far: 3.020000 # loops : 50 mean,max change (kT/e) : 6.3026177E-06 7.0381165E-04 energy calculations done at 3.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.190000 DelPhi exited at 14:00:51 3.194u 0.164s 0:03.85 87.0% 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 Mon Oct 10 2011 at 14:00:51 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 = 2724 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: 1.718036 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): -20.79700 41.36700 ymin,ymax (A): -12.62900 44.53300 zmin,zma (A): -1.779000 52.49800 x,y,z range (A): 62.16399 57.16200 54.27700 scale (grids/A): 1.718036 object centre (A): 10.28500 15.95200 25.35950 number of atom coordinates read : 2724 total number of charged atoms : 2578 net assigned charge : 11.00002 assigned positive charge : 397.8381 centred at (gu) : 95.16946 93.46808 79.89604 assigned negative charge : -386.8386 centred at (gu) : 95.57976 93.71633 79.18364 start vw surface at 0.1500000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 65008 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29873 grid for indexing accessible points = 1.400000 m= 19896 mr = 39467 m= 2355 mr = 12515 m= 92 mr = 975 m= 0 mr = 7 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.4800000 number of dielectric boundary points 34387 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 289 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 19958 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) : 0.5726788 object centre at (A) : 10.28500 15.95200 25.35950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.5166318E-04 1.3386349E-02 midg,1,midg; midg,igrid,midg 2.4242895E-02 2.2090517E-02 1,midg,midg; igrid,midg,midg 1.0871582E-02 -1.6151389E-02 gauss-seidel spectral radius is 0.9983538 estimated iterations to convergence 196 setup time was (sec) 0.7700000 now iterating at: 14:00:52 rms-change max change #iterations 3.408841 165.9155 at 10iterations 1.464706 55.75956 at 20iterations 0.6373171 23.51617 at 30iterations 0.2746910 10.13349 at 40iterations 0.1184365 4.157318 at 50iterations 5.1453959E-02 1.703636 at 60iterations 2.2246296E-02 0.8126450 at 70iterations 9.6407225E-03 0.3424950 at 80iterations 4.1827327E-03 0.1570325 at 90iterations 1.8062945E-03 7.8153610E-02 at 100iterations 7.8733993E-04 2.8816700E-02 at 110iterations 3.4213520E-04 1.4118195E-02 at 120iterations finished qdiffx linear iterations at : 14:00:59 total time elapsed so far: 7.330000 # loops : 120 mean,max change (kT/e) : 3.4213520E-04 1.4118195E-02 energy calculations done at 7.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.560000 DelPhi exited at 14:01:00 7.565u 0.211s 0:09.26 83.9% 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 14:01:02 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 = 2724 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 grid size : 179 scale,in grids/A, set to be: 2.577055 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): -20.79700 41.36700 ymin,ymax (A): -12.62900 44.53300 zmin,zma (A): -1.779000 52.49800 x,y,z range (A): 62.16399 57.16200 54.27700 scale (grids/A): 2.577055 object centre (A): 10.28500 15.95200 25.35950 number of atom coordinates read : 2724 total number of charged atoms : 2578 net assigned charge : 11.00002 assigned positive charge : 397.8381 centred at (gu) : 97.75410 95.20198 74.84388 assigned negative charge : -386.8386 centred at (gu) : 98.36956 95.57451 73.77550 start vw surface at 0.2500000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 150562 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29873 grid for indexing accessible points = 1.400000 m= 66557 mr = 97765 m= 20364 mr = 49533 m= 3616 mr = 14198 m= 317 mr = 2111 m= 2 mr = 111 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 39 time to turn everything in is 1.240000 number of dielectric boundary points 77700 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 20614 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) : 1.718036 object centre at (A) : 10.28500 15.95200 25.35950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1328682E-02 0.1408231 midg,1,midg; midg,igrid,midg 0.4384716 0.2554023 1,midg,midg; igrid,midg,midg 0.1890162 -0.4201808 gauss-seidel spectral radius is 0.9991942 estimated iterations to convergence 278 setup time was (sec) 1.520000 now iterating at: 14:01:03 rms-change max change #iterations 8.911848 296.7472 at 10iterations 5.235670 151.9590 at 20iterations 3.042710 83.21072 at 30iterations 1.745973 46.78725 at 40iterations 0.9955060 28.51699 at 50iterations 0.5668026 14.30702 at 60iterations 0.3211301 7.776764 at 70iterations 0.1819618 5.054655 at 80iterations 0.1026989 2.340947 at 90iterations 5.7817895E-02 1.347132 at 100iterations 3.2671586E-02 0.7283630 at 110iterations 1.8358314E-02 0.4320357 at 120iterations 1.0298102E-02 0.2342367 at 130iterations 5.7906313E-03 0.1222744 at 140iterations 3.2466080E-03 6.9167614E-02 at 150iterations 1.8198936E-03 4.0252686E-02 at 160iterations 1.0233152E-03 2.1304846E-02 at 170iterations 5.7536084E-04 1.3576508E-02 at 180iterations finished qdiffx linear iterations at : 14:01:13 total time elapsed so far: 10.91000 # loops : 180 mean,max change (kT/e) : 5.7536084E-04 1.3576508E-02 energy calculations done at 10.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.07000 DelPhi exited at 14:01:14 11.076u 0.195s 0:12.63 89.1% 0+0k 0+0io 0pf+0w