Sun Oct 9 18:12:56 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 Sun Oct 9 2011 at 18:12:56 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 = 2896 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: 0.5581424 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): -8.079000 55.70400 ymin,ymax (A): -14.47000 34.13800 zmin,zma (A): 22.38600 70.43400 x,y,z range (A): 63.78300 48.60800 48.04800 scale (grids/A): 0.5581424 object centre (A): 23.81250 9.834001 46.41000 number of atom coordinates read : 2896 total number of charged atoms : 2752 net assigned charge : 6.000026 assigned positive charge : 440.7544 centred at (gu) : 90.25391 90.65981 88.65849 assigned negative charge : -434.7553 centred at (gu) : 90.31194 90.74744 88.58014 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5950 nv = 96 ne = 84 npr = 57135 no. pairs analyzed = 57135 no. exposed pairs = 3799 no. arc points = 26334 no. surface atoms = 1287 nbur = 1609 mkacc time = 9.9999994E-02 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 = 1.540000 m= 265 mr = 3016 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3197 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2671 ## 317 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 7640 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.7178218E-10 1.0147426E-09 midg,1,midg; midg,igrid,midg 1.2724199E-09 -3.3624556E-10 1,midg,midg; igrid,midg,midg 1.1268430E-09 2.3597678E-11 gauss-seidel spectral radius is 0.9834369 estimated iterations to convergence 64 setup time was (sec) 0.3900000 now iterating at: 18:12:57 rms-change max change #iterations 7.8333221E-02 13.20391 at 10iterations 5.7738912E-03 0.9941730 at 20iterations 7.3981355E-04 0.1164131 at 30iterations 2.6450795E-04 3.5467148E-02 at 40iterations 1.2914740E-04 1.8447876E-02 at 50iterations finished qdiffx linear iterations at : 18:12:59 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 1.2914740E-04 1.8447876E-02 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 18:13:00 3.454u 0.175s 0:03.90 92.8% 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 Sun Oct 9 2011 at 18:13:00 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 = 2896 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: 1.674427 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): -8.079000 55.70400 ymin,ymax (A): -14.47000 34.13800 zmin,zma (A): 22.38600 70.43400 x,y,z range (A): 63.78300 48.60800 48.04800 scale (grids/A): 1.674427 object centre (A): 23.81250 9.834001 46.41000 number of atom coordinates read : 2896 total number of charged atoms : 2752 net assigned charge : 6.000026 assigned positive charge : 440.7544 centred at (gu) : 90.76128 91.97868 85.97486 assigned negative charge : -434.7553 centred at (gu) : 90.93545 92.24197 85.74021 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 65795 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26334 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 21792 mr = 44539 m= 2641 mr = 14753 m= 93 mr = 1302 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 29714 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 268 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 21234 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) : 0.5581424 object centre at (A) : 23.81250 9.834001 46.41000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.2160625E-03 6.4234645E-03 midg,1,midg; midg,igrid,midg 9.7262925E-03 -8.0248797E-03 1,midg,midg; igrid,midg,midg 2.3525514E-02 -5.5790897E-03 gauss-seidel spectral radius is 0.9982690 estimated iterations to convergence 191 setup time was (sec) 0.5500000 now iterating at: 18:13:01 rms-change max change #iterations 3.516662 153.9883 at 10iterations 1.485696 54.43758 at 20iterations 0.6353270 21.89268 at 30iterations 0.2717151 9.489325 at 40iterations 0.1161512 4.201611 at 50iterations 4.9632218E-02 1.620557 at 60iterations 2.1253765E-02 0.8256552 at 70iterations 9.1271400E-03 0.3019865 at 80iterations 3.9480110E-03 0.1715431 at 90iterations 1.7756120E-03 6.9135666E-02 at 100iterations 8.6346798E-04 3.2076836E-02 at 110iterations 4.9040373E-04 1.7570972E-02 at 120iterations finished qdiffx linear iterations at : 18:13:08 total time elapsed so far: 7.660000 # loops : 120 mean,max change (kT/e) : 4.9040373E-04 1.7570972E-02 energy calculations done at 7.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.770000 DelPhi exited at 18:13:08 7.776u 0.218s 0:08.26 96.6% 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 Sun Oct 9 2011 at 18:13:08 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 = 2896 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: 2.511641 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): -8.079000 55.70400 ymin,ymax (A): -14.47000 34.13800 zmin,zma (A): 22.38600 70.43400 x,y,z range (A): 63.78300 48.60800 48.04800 scale (grids/A): 2.511641 object centre (A): 23.81250 9.834001 46.41000 number of atom coordinates read : 2896 total number of charged atoms : 2752 net assigned charge : 6.000026 assigned positive charge : 440.7544 centred at (gu) : 91.14178 92.96791 83.96224 assigned negative charge : -434.7553 centred at (gu) : 91.40308 93.36286 83.61017 start vw surface at 0.1100000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 152322 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26334 grid for indexing accessible points = 1.400000 m= 73535 mr = 109040 m= 22952 mr = 57568 m= 4264 mr = 16984 m= 401 mr = 2710 m= 7 mr = 186 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8200000 number of dielectric boundary points 66994 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 10 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 22001 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) : 1.674427 object centre at (A) : 23.81250 9.834001 46.41000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.6388190E-02 7.3737092E-02 midg,1,midg; midg,igrid,midg 0.1633254 -0.1590859 1,midg,midg; igrid,midg,midg 0.8881868 -7.0262626E-02 gauss-seidel spectral radius is 0.9991639 estimated iterations to convergence 273 setup time was (sec) 1.050000 now iterating at: 18:13:09 rms-change max change #iterations 9.038581 261.9569 at 10iterations 5.174456 148.5293 at 20iterations 2.947198 80.48945 at 30iterations 1.665187 41.42333 at 40iterations 0.9383014 22.43317 at 50iterations 0.5262898 12.35082 at 60iterations 0.2951866 7.438387 at 70iterations 0.1652671 3.879566 at 80iterations 9.2442997E-02 1.998060 at 90iterations 5.1712476E-02 1.044083 at 100iterations 2.8834680E-02 0.6757436 at 110iterations 1.6135456E-02 0.3481913 at 120iterations 9.0116132E-03 0.2022629 at 130iterations 5.0230268E-03 0.1056595 at 140iterations 2.8089883E-03 6.1907768E-02 at 150iterations 1.5831370E-03 3.2636762E-02 at 160iterations 8.9958607E-04 2.0053864E-02 at 170iterations 5.2287779E-04 1.1428833E-02 at 180iterations finished qdiffx linear iterations at : 18:13:21 total time elapsed so far: 12.18000 # loops : 180 mean,max change (kT/e) : 5.2287779E-04 1.1428833E-02 energy calculations done at 12.18000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.32000 DelPhi exited at 18:13:21 12.318u 0.205s 0:12.78 97.8% 0+0k 0+0io 0pf+0w