Sat Oct 15 13:38:28 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 Sat Oct 15 2011 at 13:38:28 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2817 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.6306689 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): -46.76500 7.938000 ymin,ymax (A): -28.99300 27.45500 zmin,zma (A): -7.866000 41.28800 x,y,z range (A): 54.70300 56.44800 49.15400 scale (grids/A): 0.6306689 object centre (A): -19.41350 -0.7690001 16.71100 number of atom coordinates read : 2817 total number of charged atoms : 2669 net assigned charge : -0.4999843 assigned positive charge : 431.9503 centred at (gu) : 90.31828 90.43644 89.57754 assigned negative charge : -432.4511 centred at (gu) : 90.49166 90.42058 89.86715 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7350 nv = 96 ne = 84 npr = 57506 no. pairs analyzed = 57506 no. exposed pairs = 3373 no. arc points = 23486 no. surface atoms = 1135 nbur = 1682 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 352 mr = 4127 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 92 time to turn everything in is 0.2100000 number of dielectric boundary points 3550 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2338 ## 220 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 9035 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0315427E-08 -2.7892352E-08 midg,1,midg; midg,igrid,midg -1.9743098E-09 1.1221312E-09 1,midg,midg; igrid,midg,midg 1.5391036E-08 -1.9668992E-08 gauss-seidel spectral radius is 0.9869907 estimated iterations to convergence 72 setup time was (sec) 0.4200000 now iterating at: 13:38:29 rms-change max change #iterations 0.1447465 21.72831 at 10iterations 1.3987916E-02 2.424475 at 20iterations 1.3720621E-03 0.1770477 at 30iterations 1.7571053E-04 3.3752441E-02 at 40iterations 4.6515110E-05 9.2668533E-03 at 50iterations finished qdiffx linear iterations at : 13:38:34 total time elapsed so far: 3.710000 # loops : 50 mean,max change (kT/e) : 4.6515110E-05 9.2668533E-03 energy calculations done at 3.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.840000 DelPhi exited at 13:38:34 3.840u 0.230s 0:06.16 66.0% 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 15 2011 at 13:38:35 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2817 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.892007 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): -46.76500 7.938000 ymin,ymax (A): -28.99300 27.45500 zmin,zma (A): -7.866000 41.28800 x,y,z range (A): 54.70300 56.44800 49.15400 scale (grids/A): 1.892007 object centre (A): -19.41350 -0.7690001 16.71100 number of atom coordinates read : 2817 total number of charged atoms : 2669 net assigned charge : -0.4999843 assigned positive charge : 431.9503 centred at (gu) : 90.95380 91.30880 88.73197 assigned negative charge : -432.4511 centred at (gu) : 91.47462 91.26151 89.60110 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 80308 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23486 grid for indexing accessible points = 1.400000 m= 27504 mr = 56840 m= 3769 mr = 20092 m= 183 mr = 2168 m= 2 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 3029 time to turn everything in is 0.4200000 number of dielectric boundary points 32621 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 153 iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 20994 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) : 0.6306689 object centre at (A) : -19.41350 -0.7690001 16.71100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5920359E-02 -8.4039420E-02 midg,1,midg; midg,igrid,midg -5.1329071E-03 -2.2163603E-03 1,midg,midg; igrid,midg,midg 5.6241263E-02 -1.8804800E-02 gauss-seidel spectral radius is 0.9986313 estimated iterations to convergence 214 setup time was (sec) 0.7000000 now iterating at: 13:38:36 rms-change max change #iterations 4.446891 170.7394 at 10iterations 2.089579 67.62652 at 20iterations 0.9803435 31.73115 at 30iterations 0.4606587 14.95781 at 40iterations 0.2154863 6.387016 at 50iterations 0.1015323 2.952918 at 60iterations 4.7524996E-02 1.425757 at 70iterations 2.2358432E-02 0.7001619 at 80iterations 1.0489869E-02 0.3263521 at 90iterations 4.9098954E-03 0.1422386 at 100iterations 2.3096127E-03 8.2771301E-02 at 110iterations 1.0835406E-03 3.2409668E-02 at 120iterations finished qdiffx linear iterations at : 13:38:49 total time elapsed so far: 8.410000 # loops : 120 mean,max change (kT/e) : 1.0835406E-03 3.2409668E-02 energy calculations done at 8.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.540000 DelPhi exited at 13:38:49 8.543u 0.295s 0:14.68 60.1% 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 15 2011 at 13:38:49 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: 293 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2817 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.838010 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): -46.76500 7.938000 ymin,ymax (A): -28.99300 27.45500 zmin,zma (A): -7.866000 41.28800 x,y,z range (A): 54.70300 56.44800 49.15400 scale (grids/A): 2.838010 object centre (A): -19.41350 -0.7690001 16.71100 number of atom coordinates read : 2817 total number of charged atoms : 2669 net assigned charge : -0.4999843 assigned positive charge : 431.9503 centred at (gu) : 91.43069 91.96308 88.09766 assigned negative charge : -432.4511 centred at (gu) : 92.21181 91.89215 89.40142 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 185951 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23486 grid for indexing accessible points = 1.400000 m= 91537 mr = 137832 m= 30581 mr = 74780 m= 6595 mr = 24136 m= 749 mr = 4703 m= 23 mr = 419 m= 0 mr = 0 time to grow re-entrant surface = 0.5700001 no. cavity mid-points inaccessible to solvent = 10235 time to turn everything in is 1.010000 number of dielectric boundary points 73566 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 21352 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) : 1.892007 object centre at (A) : -19.41350 -0.7690001 16.71100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2278797 -1.125156 midg,1,midg; midg,igrid,midg -0.1661285 -0.1433498 1,midg,midg; igrid,midg,midg 0.4633605 -0.4545824 gauss-seidel spectral radius is 0.9992607 estimated iterations to convergence 290 setup time was (sec) 1.250000 now iterating at: 13:38:52 rms-change max change #iterations 10.47153 300.3348 at 10iterations 6.174722 154.0614 at 20iterations 3.617818 76.83183 at 30iterations 2.108556 40.14812 at 40iterations 1.226155 25.71107 at 50iterations 0.7124743 14.86312 at 60iterations 0.4131205 7.631272 at 70iterations 0.2389322 3.995613 at 80iterations 0.1380194 2.610714 at 90iterations 7.9546556E-02 1.477388 at 100iterations 4.5993548E-02 0.8801661 at 110iterations 2.6493583E-02 0.4821382 at 120iterations 1.5278097E-02 0.2560081 at 130iterations 8.8157775E-03 0.1689796 at 140iterations 5.0844653E-03 8.5586548E-02 at 150iterations 2.9328226E-03 5.3222656E-02 at 160iterations 1.6973692E-03 3.3813477E-02 at 170iterations 9.8658726E-04 1.7332077E-02 at 180iterations finished qdiffx linear iterations at : 13:39:13 total time elapsed so far: 13.68000 # loops : 180 mean,max change (kT/e) : 9.8658726E-04 1.7332077E-02 energy calculations done at 13.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.80000 DelPhi exited at 13:39:14 13.806u 0.277s 0:24.75 56.8% 0+0k 0+0io 0pf+0w