Sat Oct 8 13:53:39 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 13:53:39 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3016 !!! WARNING: NAP 500 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6444605 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): -12.20300 43.03700 ymin,ymax (A): -22.80800 21.83300 zmin,zma (A): -6.490000 47.49800 x,y,z range (A): 55.24000 44.64100 53.98800 scale (grids/A): 0.6444605 object centre (A): 15.41700 -0.4875002 20.50400 number of atom coordinates read : 3016 total number of charged atoms : 2869 net assigned charge : 7.1674585E-06 assigned positive charge : 452.1886 centred at (gu) : 88.68843 89.62247 91.21093 assigned negative charge : -452.1894 centred at (gu) : 88.65690 89.51543 91.12554 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8233 nv = 96 ne = 84 npr = 63735 no. pairs analyzed = 63735 no. exposed pairs = 3411 no. arc points = 23543 no. surface atoms = 1160 nbur = 1856 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 468 mr = 4840 m= 1 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.3100000 number of dielectric boundary points 3807 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2331 ## 232 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 10047 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0163879E-08 1.6819241E-08 midg,1,midg; midg,igrid,midg -1.7991152E-08 1.4882709E-08 1,midg,midg; igrid,midg,midg -6.4715358E-09 3.6058367E-09 gauss-seidel spectral radius is 0.9875531 estimated iterations to convergence 73 setup time was (sec) 0.5200000 now iterating at: 13:53:39 rms-change max change #iterations 0.1618025 21.27639 at 10iterations 1.6864268E-02 1.993900 at 20iterations 1.8089256E-03 0.2429123 at 30iterations 2.3513875E-04 2.7772903E-02 at 40iterations 4.0360330E-05 5.4426193E-03 at 50iterations finished qdiffx linear iterations at : 13:53:42 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 4.0360330E-05 5.4426193E-03 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 13:53:42 3.125u 0.135s 0:03.57 91.0% 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 Sat Oct 8 2011 at 13:53:42 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3016 !!! WARNING: NAP 500 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.933382 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): -12.20300 43.03700 ymin,ymax (A): -22.80800 21.83300 zmin,zma (A): -6.490000 47.49800 x,y,z range (A): 55.24000 44.64100 53.98800 scale (grids/A): 1.933382 object centre (A): 15.41700 -0.4875002 20.50400 number of atom coordinates read : 3016 total number of charged atoms : 2869 net assigned charge : 7.1674585E-06 assigned positive charge : 452.1886 centred at (gu) : 86.06482 88.86697 93.63236 assigned negative charge : -452.1894 centred at (gu) : 85.97062 88.54620 93.37653 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 89520 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23543 grid for indexing accessible points = 1.400000 m= 33046 mr = 64813 m= 5231 mr = 24897 m= 311 mr = 3264 m= 4 mr = 97 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 98 time to turn everything in is 0.5900000 number of dielectric boundary points 35041 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 147 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 22640 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) : 0.6444605 object centre at (A) : 15.41700 -0.4875002 20.50400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2899561E-02 2.7545271E-02 midg,1,midg; midg,igrid,midg 2.6551422E-03 1.9386092E-02 1,midg,midg; igrid,midg,midg -5.9372362E-02 1.2036319E-02 gauss-seidel spectral radius is 0.9987035 estimated iterations to convergence 220 setup time was (sec) 0.8500000 now iterating at: 13:53:43 rms-change max change #iterations 4.784935 209.8998 at 10iterations 2.297640 72.86277 at 20iterations 1.094699 32.90234 at 30iterations 0.5248134 15.87351 at 40iterations 0.2499223 7.766305 at 50iterations 0.1198011 3.298177 at 60iterations 5.7308458E-02 1.528368 at 70iterations 2.7487449E-02 0.7718277 at 80iterations 1.3158577E-02 0.3861237 at 90iterations 6.2844791E-03 0.1747131 at 100iterations 3.0145582E-03 8.3215714E-02 at 110iterations 1.4477232E-03 4.0922403E-02 at 120iterations finished qdiffx linear iterations at : 13:53:50 total time elapsed so far: 7.240000 # loops : 120 mean,max change (kT/e) : 1.4477232E-03 4.0922403E-02 energy calculations done at 7.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.410000 DelPhi exited at 13:53:50 7.417u 0.172s 0:07.91 95.8% 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 13:53:50 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3016 !!! WARNING: NAP 500 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.900072 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): -12.20300 43.03700 ymin,ymax (A): -22.80800 21.83300 zmin,zma (A): -6.490000 47.49800 x,y,z range (A): 55.24000 44.64100 53.98800 scale (grids/A): 2.900072 object centre (A): 15.41700 -0.4875002 20.50400 number of atom coordinates read : 3016 total number of charged atoms : 2869 net assigned charge : 7.1674585E-06 assigned positive charge : 452.1886 centred at (gu) : 84.09705 88.30021 95.44844 assigned negative charge : -452.1894 centred at (gu) : 83.95580 87.81928 95.06485 start vw surface at 0.1500000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 207174 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23543 grid for indexing accessible points = 1.400000 m= 107378 mr = 156514 m= 39049 mr = 89439 m= 9486 mr = 31644 m= 1328 mr = 7155 m= 57 mr = 846 m= 1 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 335 time to turn everything in is 1.530000 number of dielectric boundary points 78858 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 22951 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) : 1.933382 object centre at (A) : 15.41700 -0.4875002 20.50400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.1375188E-02 0.4537841 midg,1,midg; midg,igrid,midg 7.2068200E-02 0.2115323 1,midg,midg; igrid,midg,midg -0.7920960 0.3042943 gauss-seidel spectral radius is 0.9992797 estimated iterations to convergence 294 setup time was (sec) 1.820000 now iterating at: 13:53:52 rms-change max change #iterations 11.02248 447.4848 at 10iterations 6.457437 142.3194 at 20iterations 3.775308 65.89151 at 30iterations 2.200586 45.71088 at 40iterations 1.279123 25.04726 at 50iterations 0.7449902 12.94043 at 60iterations 0.4315768 7.922913 at 70iterations 0.2515824 4.220289 at 80iterations 0.1458389 2.433510 at 90iterations 8.4629260E-02 1.405993 at 100iterations 4.9042456E-02 0.8711224 at 110iterations 2.8439458E-02 0.4745674 at 120iterations 1.6537175E-02 0.2750411 at 130iterations 9.5934756E-03 0.1474380 at 140iterations 5.5671791E-03 8.9048386E-02 at 150iterations 3.2467956E-03 5.3856850E-02 at 160iterations 1.8970174E-03 3.1166077E-02 at 170iterations 1.1134219E-03 1.8440247E-02 at 180iterations finished qdiffx linear iterations at : 13:54:02 total time elapsed so far: 12.01000 # loops : 180 mean,max change (kT/e) : 1.1134219E-03 1.8440247E-02 energy calculations done at 12.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.18000 DelPhi exited at 13:54:03 12.187u 0.172s 0:12.65 97.6% 0+0k 0+0io 0pf+0w