Sun Oct 9 23:43:58 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 Sun Oct 9 2011 at 23:43:58 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: 260 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 : 429.0316 centred at (gu) : 89.80016 89.64046 89.78701 assigned negative charge : -423.0325 centred at (gu) : 89.85635 89.70824 89.71102 start vw surface at 0.1000000 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 = 9.0000004E-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 = 9.9999994E-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 0.2800000 number of grid points assigned charge 6739 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.8830545E-11 4.1443890E-10 midg,1,midg; midg,igrid,midg 4.5015439E-10 -3.2997761E-11 1,midg,midg; igrid,midg,midg 3.9254122E-10 2.2150810E-12 gauss-seidel spectral radius is 0.9815927 estimated iterations to convergence 61 setup time was (sec) 0.4000000 now iterating at: 23:43:59 rms-change max change #iterations 6.0125209E-02 14.95336 at 10iterations 3.5977559E-03 0.7535286 at 20iterations 2.2044267E-04 4.7405243E-02 at 30iterations 1.3709097E-05 2.5529861E-03 at 40iterations 8.8675233E-07 1.9073486E-04 at 50iterations finished qdiffx linear iterations at : 23:44:02 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 8.8675233E-07 1.9073486E-04 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 23:44:02 3.468u 0.354s 0:04.31 88.3% 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 Sun Oct 9 2011 at 23:44:02 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: 260 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 : 429.0316 centred at (gu) : 89.39980 88.92085 89.36060 assigned negative charge : -423.0325 centred at (gu) : 89.56904 89.12431 89.13304 start vw surface at 0.1000000 fill in re-entrant regions at 0.1500000 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 = 0.1200000 no. cavity mid-points inaccessible to solvent = 863 time to turn everything in is 0.2800000 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 0.3500000 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 -1.6855708E-03 2.2085749E-03 midg,1,midg; midg,igrid,midg 7.4251350E-03 1.6875314E-03 1,midg,midg; igrid,midg,midg 1.3207186E-02 3.0974974E-03 gauss-seidel spectral radius is 0.9980580 estimated iterations to convergence 180 setup time was (sec) 0.4900000 now iterating at: 23:44:03 rms-change max change #iterations 3.029823 157.5431 at 10iterations 1.216894 48.88168 at 20iterations 0.4911515 20.77707 at 30iterations 0.1978711 8.313421 at 40iterations 7.9399213E-02 3.351428 at 50iterations 3.2193691E-02 1.319378 at 60iterations 1.2949100E-02 0.5253944 at 70iterations 5.2358517E-03 0.2174339 at 80iterations 2.1100857E-03 7.9306602E-02 at 90iterations 8.5403968E-04 3.7462562E-02 at 100iterations 3.4388911E-04 1.4075279E-02 at 110iterations 1.3940201E-04 6.0901642E-03 at 120iterations finished qdiffx linear iterations at : 23:44:11 total time elapsed so far: 7.740000 # loops : 120 mean,max change (kT/e) : 1.3940201E-04 6.0901642E-03 energy calculations done at 7.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 23:44:11 7.877u 0.790s 0:08.97 96.5% 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 23:44:11 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: 260 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 : 429.0316 centred at (gu) : 89.09961 88.38109 89.04074 assigned negative charge : -423.0325 centred at (gu) : 89.35354 88.68636 88.69955 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2600000 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 0.6700000 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 0.7600000 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 -1.2696250E-02 2.1469906E-02 midg,1,midg; midg,igrid,midg 0.1121146 4.7566026E-02 1,midg,midg; igrid,midg,midg 6.8106495E-02 -4.0384866E-03 gauss-seidel spectral radius is 0.9990910 estimated iterations to convergence 262 setup time was (sec) 0.9100000 now iterating at: 23:44:13 rms-change max change #iterations 7.850440 242.7618 at 10iterations 4.255247 105.1639 at 20iterations 2.301694 55.01797 at 30iterations 1.243532 32.30272 at 40iterations 0.6718809 15.48894 at 50iterations 0.3622774 8.644990 at 60iterations 0.1955086 4.675889 at 70iterations 0.1054358 2.378067 at 80iterations 5.6659900E-02 1.471960 at 90iterations 3.0670619E-02 0.7378922 at 100iterations 1.6477374E-02 0.3853912 at 110iterations 8.9184465E-03 0.2131604 at 120iterations 4.7989651E-03 0.1157017 at 130iterations 2.5854823E-03 6.1276436E-02 at 140iterations 1.3954907E-03 3.7395298E-02 at 150iterations 7.5102370E-04 1.6541481E-02 at 160iterations 4.0511438E-04 9.1018677E-03 at 170iterations 2.1859916E-04 5.0964355E-03 at 180iterations finished qdiffx linear iterations at : 23:44:25 total time elapsed so far: 13.10000 # loops : 180 mean,max change (kT/e) : 2.1859916E-04 5.0964355E-03 energy calculations done at 13.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.23000 DelPhi exited at 23:44:25 13.232u 0.226s 0:14.08 95.5% 0+0k 0+0io 0pf+0w