Mon Oct 10 16:05:50 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 Mon Oct 10 2011 at 16:05:50 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4791 !!! WARNING: GLM 134 has a net charge of -0.0940 !!! WARNING: HIR 295 has a net charge of 0.5140 !!! WARNING: HIR 299 has a net charge of 0.5140 !!! WARNING: ASP 610 has a net charge of -2.0000 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: 0.5523319 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): 7.816000 62.69400 ymin,ymax (A): 52.19800 116.3810 zmin,zma (A): -35.31400 29.14000 x,y,z range (A): 54.87800 64.18301 64.45400 scale (grids/A): 0.5523319 object centre (A): 35.25500 84.28951 -3.087002 number of atom coordinates read : 4791 total number of charged atoms : 4628 net assigned charge : 1.934016 assigned positive charge : 724.9196 centred at (gu) : 89.61167 89.93535 91.34452 assigned negative charge : -722.9901 centred at (gu) : 89.57292 89.94218 91.34429 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 9307 nv = 96 ne = 84 npr = 99318 no. pairs analyzed = 99318 no. exposed pairs = 5729 no. arc points = 38808 no. surface atoms = 1940 nbur = 2851 mkacc time = 0.2600000 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 = 1.568000 m= 387 mr = 5207 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5100000 number of dielectric boundary points 4471 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3967 ## 500 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 12339 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1112336E-10 2.1923642E-10 midg,1,midg; midg,igrid,midg 2.5269542E-10 6.1528886E-11 1,midg,midg; igrid,midg,midg -4.1466702E-10 6.1973182E-10 gauss-seidel spectral radius is 0.9832242 estimated iterations to convergence 64 setup time was (sec) 0.7600000 now iterating at: 16:05:51 rms-change max change #iterations 0.1032684 14.99665 at 10iterations 8.0121187E-03 1.327236 at 20iterations 1.4505485E-03 0.2236004 at 30iterations 5.8370014E-04 7.8552246E-02 at 40iterations 2.5616155E-04 3.3298492E-02 at 50iterations finished qdiffx linear iterations at : 16:05:55 total time elapsed so far: 4.480000 # loops : 50 mean,max change (kT/e) : 2.5616155E-04 3.3298492E-02 energy calculations done at 4.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.640000 DelPhi exited at 16:05:56 4.648u 0.404s 0:05.33 94.5% 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 Mon Oct 10 2011 at 16:05:56 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4791 !!! WARNING: GLM 134 has a net charge of -0.0940 !!! WARNING: HIR 295 has a net charge of 0.5140 !!! WARNING: HIR 299 has a net charge of 0.5140 !!! WARNING: ASP 610 has a net charge of -2.0000 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: 1.656996 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): 7.816000 62.69400 ymin,ymax (A): 52.19800 116.3810 zmin,zma (A): -35.31400 29.14000 x,y,z range (A): 54.87800 64.18301 64.45400 scale (grids/A): 1.656996 object centre (A): 35.25500 84.28951 -3.087002 number of atom coordinates read : 4791 total number of charged atoms : 4628 net assigned charge : 1.934016 assigned positive charge : 724.9196 centred at (gu) : 88.83321 89.80428 94.03184 assigned negative charge : -722.9901 centred at (gu) : 88.71806 89.82598 94.03243 start vw surface at 0.1700000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 104240 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38808 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 33373 mr = 74558 m= 3722 mr = 23488 m= 119 mr = 1928 m= 0 mr = 13 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 2738 time to turn everything in is 0.8300000 number of dielectric boundary points 41467 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 418 ## 1 charges are in solution ## iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 35576 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) : 0.5523319 object centre at (A) : 35.25500 84.28951 -3.087002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.8511487E-02 8.1519382E-03 midg,1,midg; midg,igrid,midg 9.2484225E-03 1.5352366E-02 1,midg,midg; igrid,midg,midg -7.4660167E-04 6.4028013E-03 gauss-seidel spectral radius is 0.9984090 estimated iterations to convergence 199 setup time was (sec) 1.230000 now iterating at: 16:05:57 rms-change max change #iterations 4.541244 161.0582 at 10iterations 2.003850 67.25774 at 20iterations 0.8835896 26.55159 at 30iterations 0.3904664 13.00362 at 40iterations 0.1721837 4.884967 at 50iterations 7.6240748E-02 2.209910 at 60iterations 3.3853900E-02 0.9584566 at 70iterations 1.5007151E-02 0.5103502 at 80iterations 6.7921225E-03 0.1946554 at 90iterations 3.1744610E-03 8.9745522E-02 at 100iterations 1.5652834E-03 4.6356201E-02 at 110iterations 8.7009388E-04 2.7446747E-02 at 120iterations finished qdiffx linear iterations at : 16:06:07 total time elapsed so far: 10.97000 # loops : 120 mean,max change (kT/e) : 8.7009388E-04 2.7446747E-02 energy calculations done at 10.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.12000 DelPhi exited at 16:06:08 11.126u 0.498s 0:11.92 97.3% 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 16:06:08 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4791 !!! WARNING: GLM 134 has a net charge of -0.0940 !!! WARNING: HIR 295 has a net charge of 0.5140 !!! WARNING: HIR 299 has a net charge of 0.5140 !!! WARNING: ASP 610 has a net charge of -2.0000 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: 2.485493 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): 7.816000 62.69400 ymin,ymax (A): 52.19800 116.3810 zmin,zma (A): -35.31400 29.14000 x,y,z range (A): 54.87800 64.18301 64.45400 scale (grids/A): 2.485493 object centre (A): 35.25500 84.28951 -3.087002 number of atom coordinates read : 4791 total number of charged atoms : 4628 net assigned charge : 1.934016 assigned positive charge : 724.9196 centred at (gu) : 88.24933 89.70602 96.04723 assigned negative charge : -722.9901 centred at (gu) : 88.07703 89.73878 96.04850 start vw surface at 0.1800000 fill in re-entrant regions at 0.6700000 boundary points on vw surface= 242904 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38808 grid for indexing accessible points = 1.400000 m= 114994 mr = 182031 m= 33798 mr = 92141 m= 5883 mr = 25860 m= 442 mr = 4007 m= 11 mr = 227 m= 0 mr = 0 time to grow re-entrant surface = 1.290000 no. cavity mid-points inaccessible to solvent = 9140 time to turn everything in is 2.110000 number of dielectric boundary points 93766 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 2.260000 number of grid points assigned charge 36984 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) : 1.656996 object centre at (A) : 35.25500 84.28951 -3.087002 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3141635 0.4236216 midg,1,midg; midg,igrid,midg 8.4815726E-02 0.3536428 1,midg,midg; igrid,midg,midg 1.8189723E-02 0.1074528 gauss-seidel spectral radius is 0.9992433 estimated iterations to convergence 287 setup time was (sec) 2.470000 now iterating at: 16:06:11 rms-change max change #iterations 11.64697 393.6848 at 10iterations 6.859385 172.0917 at 20iterations 4.018218 87.12421 at 30iterations 2.345823 47.72110 at 40iterations 1.363061 25.33038 at 50iterations 0.7906796 13.37753 at 60iterations 0.4569930 8.072271 at 70iterations 0.2628742 4.572635 at 80iterations 0.1516594 2.592144 at 90iterations 8.7229870E-02 1.597372 at 100iterations 5.0194036E-02 1.045792 at 110iterations 2.8806286E-02 0.4852600 at 120iterations 1.6589925E-02 0.2715073 at 130iterations 9.5892642E-03 0.1602402 at 140iterations 5.5737318E-03 0.1134939 at 150iterations 3.2859670E-03 5.1712751E-02 at 160iterations 1.9789671E-03 3.1917572E-02 at 170iterations 1.2428412E-03 2.0202637E-02 at 180iterations finished qdiffx linear iterations at : 16:06:29 total time elapsed so far: 20.81000 # loops : 180 mean,max change (kT/e) : 1.2428412E-03 2.0202637E-02 energy calculations done at 20.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.97000 DelPhi exited at 16:06:29 20.971u 0.480s 0:21.73 98.7% 0+0k 0+0io 0pf+0w