Sun Oct 9 23:43:31 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 23:43:31 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 = 2801 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: 0.5291320 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): -40.97200 26.30800 ymin,ymax (A): -26.50700 23.86500 zmin,zma (A): -7.676000 34.85600 x,y,z range (A): 67.28000 50.37200 42.53200 scale (grids/A): 0.5291320 object centre (A): -7.332000 -1.321000 13.59000 number of atom coordinates read : 2801 total number of charged atoms : 2659 net assigned charge : 6.000009 assigned positive charge : 427.0316 centred at (gu) : 89.79395 89.65224 89.78907 assigned negative charge : -421.0326 centred at (gu) : 89.85089 89.72307 89.71487 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5073 nv = 96 ne = 84 npr = 53911 no. pairs analyzed = 53911 no. exposed pairs = 3768 no. arc points = 27870 no. surface atoms = 1248 nbur = 1553 mkacc time = 8.9999996E-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 = 1.624000 m= 200 mr = 2337 m= 1 mr = 4 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 2933 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2826 ## 433 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 6739 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.1246418E-11 4.0806145E-10 midg,1,midg; midg,igrid,midg 4.5840035E-10 -4.1524225E-11 1,midg,midg; igrid,midg,midg 3.9475995E-10 6.5790326E-13 gauss-seidel spectral radius is 0.9815927 estimated iterations to convergence 61 setup time was (sec) 0.4000000 now iterating at: 23:43:31 rms-change max change #iterations 5.9161000E-02 14.95312 at 10iterations 3.5336874E-03 0.7626057 at 20iterations 2.1622669E-04 4.7325134E-02 at 30iterations 1.3450142E-05 2.7542114E-03 at 40iterations 8.6539518E-07 1.9454956E-04 at 50iterations finished qdiffx linear iterations at : 23:43:34 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 8.6539518E-07 1.9454956E-04 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 23:43:35 3.490u 0.183s 0:04.00 91.7% 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 23:43:35 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2801 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: 1.587396 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): -40.97200 26.30800 ymin,ymax (A): -26.50700 23.86500 zmin,zma (A): -7.676000 34.85600 x,y,z range (A): 67.28000 50.37200 42.53200 scale (grids/A): 1.587396 object centre (A): -7.332000 -1.321000 13.59000 number of atom coordinates read : 2801 total number of charged atoms : 2659 net assigned charge : 6.000009 assigned positive charge : 427.0316 centred at (gu) : 89.38120 88.95621 89.36671 assigned negative charge : -421.0326 centred at (gu) : 89.55270 89.16880 89.14459 start vw surface at 0.1000000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 56364 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27870 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 15155 mr = 35769 m= 1288 mr = 9737 m= 36 mr = 483 m= 0 mr = 2 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 863 time to turn everything in is 0.2900000 number of dielectric boundary points 26852 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 402 ## 7 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 20230 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) : 0.5291320 object centre at (A) : -7.332000 -1.321000 13.59000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6206530E-03 2.0880273E-03 midg,1,midg; midg,igrid,midg 7.6706409E-03 1.6359497E-03 1,midg,midg; igrid,midg,midg 1.3260689E-02 3.0634438E-03 gauss-seidel spectral radius is 0.9980580 estimated iterations to convergence 180 setup time was (sec) 0.5200000 now iterating at: 23:43:36 rms-change max change #iterations 3.011868 157.5431 at 10iterations 1.209403 48.88168 at 20iterations 0.4881602 20.31304 at 30iterations 0.1966704 8.152283 at 40iterations 7.8938097E-02 3.305009 at 50iterations 3.2004829E-02 1.293742 at 60iterations 1.2872180E-02 0.5216084 at 70iterations 5.2045295E-03 0.2151680 at 80iterations 2.0967668E-03 7.8208923E-02 at 90iterations 8.4938126E-04 3.7186384E-02 at 100iterations 3.4189221E-04 1.3961792E-02 at 110iterations 1.3852169E-04 6.1836243E-03 at 120iterations finished qdiffx linear iterations at : 23:43:43 total time elapsed so far: 8.260000 # loops : 120 mean,max change (kT/e) : 1.3852169E-04 6.1836243E-03 energy calculations done at 8.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.400000 DelPhi exited at 23:43:44 8.398u 0.222s 0:09.02 95.4% 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 23:43:44 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 = 2801 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: 2.381094 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): -40.97200 26.30800 ymin,ymax (A): -26.50700 23.86500 zmin,zma (A): -7.676000 34.85600 x,y,z range (A): 67.28000 50.37200 42.53200 scale (grids/A): 2.381094 object centre (A): -7.332000 -1.321000 13.59000 number of atom coordinates read : 2801 total number of charged atoms : 2659 net assigned charge : 6.000009 assigned positive charge : 427.0316 centred at (gu) : 89.07169 88.43412 89.04992 assigned negative charge : -421.0326 centred at (gu) : 89.32902 88.75309 88.71687 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 131152 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27870 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 54569 mr = 88632 m= 13702 mr = 41342 m= 1782 mr = 9808 m= 89 mr = 980 m= 0 mr = 20 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 2828 time to turn everything in is 0.6500000 number of dielectric boundary points 60512 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 27 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 21232 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) : 1.587396 object centre at (A) : -7.332000 -1.321000 13.59000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1856650E-02 1.9619694E-02 midg,1,midg; midg,igrid,midg 0.1159674 4.6798900E-02 1,midg,midg; igrid,midg,midg 6.8985492E-02 -4.7684512E-03 gauss-seidel spectral radius is 0.9990910 estimated iterations to convergence 262 setup time was (sec) 0.8800000 now iterating at: 23:43:45 rms-change max change #iterations 7.807876 242.7618 at 10iterations 4.231900 105.1640 at 20iterations 2.288705 55.66378 at 30iterations 1.236876 31.21738 at 40iterations 0.6683288 15.61307 at 50iterations 0.3603445 8.627884 at 60iterations 0.1944951 4.572545 at 70iterations 0.1048643 2.385651 at 80iterations 5.6352168E-02 1.475562 at 90iterations 3.0512296E-02 0.7394142 at 100iterations 1.6394882E-02 0.3821564 at 110iterations 8.8705225E-03 0.2115054 at 120iterations 4.7739781E-03 0.1145549 at 130iterations 2.5721979E-03 6.1093330E-02 at 140iterations 1.3884451E-03 3.7668705E-02 at 150iterations 7.4705237E-04 1.6714096E-02 at 160iterations 4.0300351E-04 9.0961456E-03 at 170iterations 2.1746435E-04 5.0506592E-03 at 180iterations finished qdiffx linear iterations at : 23:43:57 total time elapsed so far: 12.92000 # loops : 180 mean,max change (kT/e) : 2.1746435E-04 5.0506592E-03 energy calculations done at 12.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.06000 DelPhi exited at 23:43:58 13.064u 0.306s 0:13.97 95.6% 0+0k 0+0io 0pf+0w