Tue Oct 11 07:51:26 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 Tue Oct 11 2011 at 07:51:26 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 = 2382 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6443672 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): -9.036000 39.85200 ymin,ymax (A): -14.38600 40.86200 zmin,zma (A): 5.247000 52.63900 x,y,z range (A): 48.88800 55.24800 47.39200 scale (grids/A): 0.6443672 object centre (A): 15.40800 13.23800 28.94300 number of atom coordinates read : 2382 total number of charged atoms : 2246 net assigned charge : 4.500007 assigned positive charge : 357.3243 centred at (gu) : 89.42634 88.53848 90.62201 assigned negative charge : -352.8248 centred at (gu) : 89.33852 88.55183 90.78178 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6726 nv = 96 ne = 84 npr = 47807 no. pairs analyzed = 47807 no. exposed pairs = 2869 no. arc points = 20073 no. surface atoms = 966 nbur = 1416 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 392 mr = 3808 m= 2 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.3300000 number of dielectric boundary points 3257 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2053 ## 213 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7892 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.3022968E-08 -1.3517171E-08 midg,1,midg; midg,igrid,midg 1.2466333E-08 4.4787796E-09 1,midg,midg; igrid,midg,midg -3.4046708E-09 1.5897241E-08 gauss-seidel spectral radius is 0.9875011 estimated iterations to convergence 73 setup time was (sec) 0.6000000 now iterating at: 07:51:27 rms-change max change #iterations 0.1406655 20.25446 at 10iterations 1.4301382E-02 2.009556 at 20iterations 1.5380761E-03 0.2421112 at 30iterations 1.8649398E-04 2.9779434E-02 at 40iterations 2.8281311E-05 4.4555664E-03 at 50iterations finished qdiffx linear iterations at : 07:51:30 total time elapsed so far: 3.930000 # loops : 50 mean,max change (kT/e) : 2.8281311E-05 4.4555664E-03 energy calculations done at 3.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.110000 DelPhi exited at 07:51:32 4.116u 0.286s 0:05.53 79.3% 0+0k 0+0io 6pf+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 Tue Oct 11 2011 at 07:51:32 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 = 2382 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.933102 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): -9.036000 39.85200 ymin,ymax (A): -14.38600 40.86200 zmin,zma (A): 5.247000 52.63900 x,y,z range (A): 48.88800 55.24800 47.39200 scale (grids/A): 1.933102 object centre (A): 15.40800 13.23800 28.94300 number of atom coordinates read : 2382 total number of charged atoms : 2246 net assigned charge : 4.500007 assigned positive charge : 357.3243 centred at (gu) : 88.27847 85.61495 91.86543 assigned negative charge : -352.8248 centred at (gu) : 88.01533 85.65542 92.34516 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 72366 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20073 grid for indexing accessible points = 1.400000 m= 27445 mr = 50956 m= 4443 mr = 20856 m= 291 mr = 2963 m= 0 mr = 102 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 1457 time to turn everything in is 0.6500000 number of dielectric boundary points 29668 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 140 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 17692 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) : 0.6443672 object centre at (A) : 15.40800 13.23800 28.94300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3455448E-02 -2.0115111E-02 midg,1,midg; midg,igrid,midg 2.7159015E-02 2.1317665E-02 1,midg,midg; igrid,midg,midg -4.5964126E-03 5.2991272E-03 gauss-seidel spectral radius is 0.9986514 estimated iterations to convergence 216 setup time was (sec) 0.9400000 now iterating at: 07:51:33 rms-change max change #iterations 4.072166 202.7980 at 10iterations 1.916271 66.17892 at 20iterations 0.9085478 29.51034 at 30iterations 0.4277283 14.99317 at 40iterations 0.2014042 6.399666 at 50iterations 9.4615415E-02 3.361576 at 60iterations 4.4735301E-02 1.359290 at 70iterations 2.1140903E-02 0.6756096 at 80iterations 9.9349385E-03 0.3254585 at 90iterations 4.6886061E-03 0.1516151 at 100iterations 2.2226204E-03 7.0559740E-02 at 110iterations 1.0514341E-03 3.2633305E-02 at 120iterations finished qdiffx linear iterations at : 07:51:42 total time elapsed so far: 9.400000 # loops : 120 mean,max change (kT/e) : 1.0514341E-03 3.2633305E-02 energy calculations done at 9.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.570000 DelPhi exited at 07:51:42 9.569u 0.339s 0:10.37 95.3% 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 Tue Oct 11 2011 at 07:51:42 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2382 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.899652 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): -9.036000 39.85200 ymin,ymax (A): -14.38600 40.86200 zmin,zma (A): 5.247000 52.63900 x,y,z range (A): 48.88800 55.24800 47.39200 scale (grids/A): 2.899652 object centre (A): 15.40800 13.23800 28.94300 number of atom coordinates read : 2382 total number of charged atoms : 2246 net assigned charge : 4.500007 assigned positive charge : 357.3243 centred at (gu) : 87.41771 83.42244 92.79800 assigned negative charge : -352.8248 centred at (gu) : 87.02293 83.48300 93.51780 start vw surface at 0.1600000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 167082 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20073 grid for indexing accessible points = 1.400000 m= 87921 mr = 122929 m= 32773 mr = 73285 m= 8217 mr = 27025 m= 1301 mr = 6315 m= 78 mr = 982 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 1.020000 no. cavity mid-points inaccessible to solvent = 5355 time to turn everything in is 1.690000 number of dielectric boundary points 66806 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.840000 number of grid points assigned charge 17965 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) : 1.933102 object centre at (A) : 15.40800 13.23800 28.94300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4809314 -0.3384827 midg,1,midg; midg,igrid,midg 0.1846204 0.2067889 1,midg,midg; igrid,midg,midg -3.0502321E-02 -1.4977293E-02 gauss-seidel spectral radius is 0.9992550 estimated iterations to convergence 289 setup time was (sec) 2.010000 now iterating at: 07:51:45 rms-change max change #iterations 9.590937 395.4551 at 10iterations 5.587099 152.5830 at 20iterations 3.237022 69.72095 at 30iterations 1.877412 37.30243 at 40iterations 1.083377 23.58466 at 50iterations 0.6232767 12.37818 at 60iterations 0.3595199 6.845840 at 70iterations 0.2064220 4.087958 at 80iterations 0.1186973 2.293947 at 90iterations 6.8351448E-02 1.261066 at 100iterations 3.9116975E-02 0.7162476 at 110iterations 2.2513039E-02 0.4255867 at 120iterations 1.2936901E-02 0.2603645 at 130iterations 7.4157454E-03 0.1347961 at 140iterations 4.2601652E-03 8.2547188E-02 at 150iterations 2.4575235E-03 4.3774605E-02 at 160iterations 1.4186085E-03 2.7294159E-02 at 170iterations 8.2146528E-04 1.5890121E-02 at 180iterations finished qdiffx linear iterations at : 07:51:58 total time elapsed so far: 15.90000 # loops : 180 mean,max change (kT/e) : 8.2146528E-04 1.5890121E-02 energy calculations done at 15.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.07000 DelPhi exited at 07:51:59 16.072u 0.321s 0:16.96 96.6% 0+0k 0+0io 0pf+0w