Sat Oct 8 17:08:46 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 Sat Oct 8 2011 at 17:08:46 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 = 3366 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: 0.5558158 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): 35.84000 93.26600 ymin,ymax (A): 16.45400 80.50400 zmin,zma (A): -21.61500 24.88700 x,y,z range (A): 57.42600 64.05000 46.50200 scale (grids/A): 0.5558158 object centre (A): 64.55300 48.47900 1.636000 number of atom coordinates read : 3366 total number of charged atoms : 3220 net assigned charge : -7.999982 assigned positive charge : 504.7726 centred at (gu) : 90.46194 90.09235 89.86156 assigned negative charge : -512.7739 centred at (gu) : 90.44816 90.04559 89.81593 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6775 nv = 96 ne = 84 npr = 67619 no. pairs analyzed = 67619 no. exposed pairs = 4248 no. arc points = 29084 no. surface atoms = 1434 nbur = 1932 mkacc time = 0.1900000 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= 318 mr = 3639 m= 2 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 3434 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2967 ## 397 charges are in solution ## iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 8854 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2750379E-09 -2.2184216E-10 midg,1,midg; midg,igrid,midg -1.2183795E-09 -2.2031744E-10 1,midg,midg; igrid,midg,midg -7.8848417E-10 -6.4221539E-10 gauss-seidel spectral radius is 0.9833350 estimated iterations to convergence 64 setup time was (sec) 0.6700000 now iterating at: 17:08:47 rms-change max change #iterations 8.5473917E-02 15.41498 at 10iterations 6.0657784E-03 1.017231 at 20iterations 4.6992255E-04 7.2692871E-02 at 30iterations 5.8269703E-05 1.1246204E-02 at 40iterations 1.2150682E-05 2.6831627E-03 at 50iterations finished qdiffx linear iterations at : 17:08:50 total time elapsed so far: 3.960000 # loops : 50 mean,max change (kT/e) : 1.2150682E-05 2.6831627E-03 energy calculations done at 3.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.140000 DelPhi exited at 17:08:50 4.140u 0.281s 0:04.68 94.4% 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 8 2011 at 17:08:50 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3366 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: 1.667447 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): 35.84000 93.26600 ymin,ymax (A): 16.45400 80.50400 zmin,zma (A): -21.61500 24.88700 x,y,z range (A): 57.42600 64.05000 46.50200 scale (grids/A): 1.667447 object centre (A): 64.55300 48.47900 1.636000 number of atom coordinates read : 3366 total number of charged atoms : 3220 net assigned charge : -7.999982 assigned positive charge : 504.7726 centred at (gu) : 91.38518 90.27628 89.58385 assigned negative charge : -512.7739 centred at (gu) : 91.34418 90.13638 89.44759 start vw surface at 0.1700000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 75178 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29084 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 24929 mr = 52100 m= 2940 mr = 17525 m= 99 mr = 1506 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 496 time to turn everything in is 0.6700000 number of dielectric boundary points 32010 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 311 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 24866 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) : 0.5558158 object centre at (A) : 64.55300 48.47900 1.636000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.8577196E-03 -3.6422054E-03 midg,1,midg; midg,igrid,midg 5.3921319E-03 1.7517412E-02 1,midg,midg; igrid,midg,midg -2.4205180E-02 -7.5831781E-03 gauss-seidel spectral radius is 0.9983026 estimated iterations to convergence 193 setup time was (sec) 0.9600000 now iterating at: 17:08:52 rms-change max change #iterations 3.728969 177.1191 at 10iterations 1.600041 58.22682 at 20iterations 0.6858554 23.57778 at 30iterations 0.2942265 11.03117 at 40iterations 0.1267000 4.301580 at 50iterations 5.4466248E-02 1.987627 at 60iterations 2.3469608E-02 0.8172016 at 70iterations 1.0079691E-02 0.3308430 at 80iterations 4.3433458E-03 0.1508636 at 90iterations 1.8754110E-03 6.7847252E-02 at 100iterations 8.1659987E-04 2.8280258E-02 at 110iterations 3.5801611E-04 1.1728287E-02 at 120iterations finished qdiffx linear iterations at : 17:09:00 total time elapsed so far: 9.240000 # loops : 120 mean,max change (kT/e) : 3.5801611E-04 1.1728287E-02 energy calculations done at 9.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.420000 DelPhi exited at 17:09:00 9.423u 0.303s 0:09.99 97.2% 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 8 2011 at 17:09:00 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 = 3366 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: 2.501171 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): 35.84000 93.26600 ymin,ymax (A): 16.45400 80.50400 zmin,zma (A): -21.61500 24.88700 x,y,z range (A): 57.42600 64.05000 46.50200 scale (grids/A): 2.501171 object centre (A): 64.55300 48.47900 1.636000 number of atom coordinates read : 3366 total number of charged atoms : 3220 net assigned charge : -7.999982 assigned positive charge : 504.7726 centred at (gu) : 92.07761 90.41410 89.37550 assigned negative charge : -512.7739 centred at (gu) : 92.01609 90.20452 89.17115 start vw surface at 0.1700000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 174670 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29084 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 84521 mr = 127190 m= 25797 mr = 67568 m= 4752 mr = 19632 m= 414 mr = 3223 m= 12 mr = 212 m= 0 mr = 0 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 1737 time to turn everything in is 1.660000 number of dielectric boundary points 72341 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 15 iepsmp to db, and charging done at 1.800000 number of grid points assigned charge 25740 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) : 1.667447 object centre at (A) : 64.55300 48.47900 1.636000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1214700 -2.5452584E-02 midg,1,midg; midg,igrid,midg 0.2391270 0.4485309 1,midg,midg; igrid,midg,midg -0.3089122 -4.6303462E-02 gauss-seidel spectral radius is 0.9991793 estimated iterations to convergence 276 setup time was (sec) 1.960000 now iterating at: 17:09:03 rms-change max change #iterations 9.516548 342.7035 at 10iterations 5.402882 131.5342 at 20iterations 3.046272 62.04824 at 30iterations 1.714182 34.43680 at 40iterations 0.9653243 19.30526 at 50iterations 0.5409252 10.04412 at 60iterations 0.3023936 6.199321 at 70iterations 0.1692983 3.714047 at 80iterations 9.4642147E-02 1.885380 at 90iterations 5.2898686E-02 0.9561579 at 100iterations 2.9525047E-02 0.5697575 at 110iterations 1.6518097E-02 0.3148575 at 120iterations 9.2225308E-03 0.1726646 at 130iterations 5.1564709E-03 0.1003480 at 140iterations 2.8947748E-03 5.4684758E-02 at 150iterations 1.6298773E-03 3.2633781E-02 at 160iterations 9.2066708E-04 1.6441345E-02 at 170iterations 5.2929844E-04 1.0360718E-02 at 180iterations finished qdiffx linear iterations at : 17:09:16 total time elapsed so far: 15.56000 # loops : 180 mean,max change (kT/e) : 5.2929844E-04 1.0360718E-02 energy calculations done at 15.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.74000 DelPhi exited at 17:09:17 15.740u 0.329s 0:16.34 98.2% 0+0k 0+0io 0pf+0w