Fri Feb 3 13:36:12 PST 2012 #!/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 Fri Feb 3 2012 at 13:36:13 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4236 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: 0.5408115 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): -3.499000 54.18600 ymin,ymax (A): 17.77000 83.59700 zmin,zma (A): -18.22600 44.93500 x,y,z range (A): 57.68500 65.82700 63.16100 scale (grids/A): 0.5408115 object centre (A): 25.34350 50.68350 13.35450 number of atom coordinates read : 4236 total number of charged atoms : 4087 net assigned charge : 2.000051 assigned positive charge : 627.1864 centred at (gu) : 90.25095 92.18813 90.13595 assigned negative charge : -625.1909 centred at (gu) : 90.31511 92.23761 90.10125 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 7957 nv = 96 ne = 84 npr = 86250 no. pairs analyzed = 86250 no. exposed pairs = 5358 no. arc points = 37290 no. surface atoms = 1833 nbur = 2403 mkacc time = 0.1500000 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= 354 mr = 4133 m= 0 mr = 17 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 4161 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3665 ## 433 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 10550 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4956636E-10 3.8832015E-10 midg,1,midg; midg,igrid,midg 2.8296279E-10 -4.7757742E-10 1,midg,midg; igrid,midg,midg 5.6102267E-10 -4.0847947E-10 gauss-seidel spectral radius is 0.9824742 estimated iterations to convergence 62 setup time was (sec) 0.5000000 now iterating at: 13:36:14 rms-change max change #iterations 8.2217351E-02 12.13229 at 10iterations 5.5524539E-03 0.8293984 at 20iterations 5.4482551E-04 8.8572502E-02 at 30iterations 1.6077865E-04 2.5308132E-02 at 40iterations 6.1725259E-05 9.6449852E-03 at 50iterations finished qdiffx linear iterations at : 13:36:17 total time elapsed so far: 3.410000 # loops : 50 mean,max change (kT/e) : 6.1725259E-05 9.6449852E-03 energy calculations done at 3.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.550000 DelPhi exited at 13:36:17 3.557u 0.177s 0:03.75 99.2% 0+0k 0+0io 8pf+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 Fri Feb 3 2012 at 13:36:17 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4236 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: 1.622435 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): -3.499000 54.18600 ymin,ymax (A): 17.77000 83.59700 zmin,zma (A): -18.22600 44.93500 x,y,z range (A): 57.68500 65.82700 63.16100 scale (grids/A): 1.622435 object centre (A): 25.34350 50.68350 13.35450 number of atom coordinates read : 4236 total number of charged atoms : 4087 net assigned charge : 2.000051 assigned positive charge : 627.1864 centred at (gu) : 90.75150 96.56245 90.40638 assigned negative charge : -625.1909 centred at (gu) : 90.94509 96.71249 90.30373 start vw surface at 0.1200000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 88440 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37290 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 27842 mr = 60133 m= 2956 mr = 19067 m= 82 mr = 1430 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 1099 time to turn everything in is 0.4400000 number of dielectric boundary points 38685 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 366 ## 4 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 31298 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) : 0.5408115 object centre at (A) : 25.34350 50.68350 13.35450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.3174708E-02 2.0294616E-03 midg,1,midg; midg,igrid,midg 9.6461745E-03 -3.3578805E-03 1,midg,midg; igrid,midg,midg -2.0120856E-03 -1.1107456E-02 gauss-seidel spectral radius is 0.9983000 estimated iterations to convergence 193 setup time was (sec) 0.6500000 now iterating at: 13:36:18 rms-change max change #iterations 4.041759 194.6746 at 10iterations 1.732147 64.47585 at 20iterations 0.7459212 24.28841 at 30iterations 0.3191570 10.79281 at 40iterations 0.1375627 5.175935 at 50iterations 5.9110835E-02 1.895306 at 60iterations 2.5426265E-02 0.7877502 at 70iterations 1.0949312E-02 0.3544693 at 80iterations 4.7396431E-03 0.1383362 at 90iterations 2.0784060E-03 6.6043854E-02 at 100iterations 9.3606918E-04 3.5044670E-02 at 110iterations 4.5027057E-04 1.6523361E-02 at 120iterations finished qdiffx linear iterations at : 13:36:25 total time elapsed so far: 7.790000 # loops : 120 mean,max change (kT/e) : 4.5027057E-04 1.6523361E-02 energy calculations done at 7.790000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.930000 DelPhi exited at 13:36:25 7.932u 0.212s 0:08.14 100.0% 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 Fri Feb 3 2012 at 13:36:25 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4236 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: 2.433652 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): -3.499000 54.18600 ymin,ymax (A): 17.77000 83.59700 zmin,zma (A): -18.22600 44.93500 x,y,z range (A): 57.68500 65.82700 63.16100 scale (grids/A): 2.433652 object centre (A): 25.34350 50.68350 13.35450 number of atom coordinates read : 4236 total number of charged atoms : 4087 net assigned charge : 2.000051 assigned positive charge : 627.1864 centred at (gu) : 91.12696 99.84318 90.60916 assigned negative charge : -625.1909 centred at (gu) : 91.41762 100.0688 90.45526 start vw surface at 0.1200000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 205739 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37290 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 95356 mr = 147665 m= 27974 mr = 74957 m= 4509 mr = 20958 m= 278 mr = 2914 m= 4 mr = 104 m= 0 mr = 0 time to grow re-entrant surface = 0.6100000 no. cavity mid-points inaccessible to solvent = 3642 time to turn everything in is 1.090000 number of dielectric boundary points 87262 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 31 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 32668 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) : 1.622435 object centre at (A) : 25.34350 50.68350 13.35450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1120510 -5.8946759E-02 midg,1,midg; midg,igrid,midg 9.6667811E-02 -0.1402259 1,midg,midg; igrid,midg,midg -7.4733295E-02 -3.7969932E-02 gauss-seidel spectral radius is 0.9992089 estimated iterations to convergence 281 setup time was (sec) 1.330000 now iterating at: 13:36:27 rms-change max change #iterations 10.51102 509.5529 at 10iterations 6.130645 163.7464 at 20iterations 3.544787 78.41428 at 30iterations 2.042211 42.05995 at 40iterations 1.170924 23.27066 at 50iterations 0.6673083 12.23180 at 60iterations 0.3798589 6.855652 at 70iterations 0.2159115 3.950569 at 80iterations 0.1225201 2.478934 at 90iterations 6.9399685E-02 1.223801 at 100iterations 3.9359611E-02 0.7314911 at 110iterations 2.2260578E-02 0.4219851 at 120iterations 1.2595607E-02 0.2205963 at 130iterations 7.1205529E-03 0.1220708 at 140iterations 4.0351255E-03 7.3914528E-02 at 150iterations 2.2889003E-03 3.9975166E-02 at 160iterations 1.3050154E-03 2.4410248E-02 at 170iterations 7.4979285E-04 1.3886452E-02 at 180iterations finished qdiffx linear iterations at : 13:36:38 total time elapsed so far: 12.93000 # loops : 180 mean,max change (kT/e) : 7.4979285E-04 1.3886452E-02 energy calculations done at 12.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.06000 DelPhi exited at 13:36:39 13.064u 0.232s 0:13.29 100.0% 0+0k 0+0io 0pf+0w