Mon Oct 10 09:16:41 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 Mon Oct 10 2011 at 09:16:41 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1044 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: 0.7400939 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): -27.20900 10.14000 ymin,ymax (A): 0.9760000 41.64400 zmin,zma (A): 11.04200 59.14400 x,y,z range (A): 37.34900 40.66800 48.10200 scale (grids/A): 0.7400939 object centre (A): -8.534500 21.31000 35.09300 number of atom coordinates read : 1044 total number of charged atoms : 918 net assigned charge : 1.500003 assigned positive charge : 146.8620 centred at (gu) : 91.76807 91.41974 91.40591 assigned negative charge : -145.3620 centred at (gu) : 91.62087 91.53273 91.07783 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 4144 nv = 96 ne = 84 npr = 20593 no. pairs analyzed = 20593 no. exposed pairs = 1542 no. arc points = 11491 no. surface atoms = 520 nbur = 524 mkacc time = 4.0000007E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 291 mr = 1980 m= 2 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 4.9999997E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 2411 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 857 ## 68 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 3942 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0048403E-07 2.2238106E-07 midg,1,midg; midg,igrid,midg 5.7702390E-08 -3.8393686E-08 1,midg,midg; igrid,midg,midg -3.1632638E-08 1.2670874E-07 gauss-seidel spectral radius is 0.9903854 estimated iterations to convergence 83 setup time was (sec) 0.4100000 now iterating at: 09:16:41 rms-change max change #iterations 0.1650175 34.04459 at 10iterations 2.1641677E-02 4.167953 at 20iterations 2.8475788E-03 0.4568543 at 30iterations 3.7573991E-04 6.4159393E-02 at 40iterations 4.9202063E-05 7.6293945E-03 at 50iterations finished qdiffx linear iterations at : 09:16:44 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 4.9202063E-05 7.6293945E-03 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 09:16:45 3.114u 0.181s 0:03.65 90.1% 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 Mon Oct 10 2011 at 09:16:45 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1044 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: 2.220282 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): -27.20900 10.14000 ymin,ymax (A): 0.9760000 41.64400 zmin,zma (A): 11.04200 59.14400 x,y,z range (A): 37.34900 40.66800 48.10200 scale (grids/A): 2.220282 object centre (A): -8.534500 21.31000 35.09300 number of atom coordinates read : 1044 total number of charged atoms : 918 net assigned charge : 1.500003 assigned positive charge : 146.8620 centred at (gu) : 95.30438 94.25927 94.21780 assigned negative charge : -145.3620 centred at (gu) : 94.86259 94.59827 93.23362 start vw surface at 0.1300000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 42515 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11491 grid for indexing accessible points = 1.400000 m= 16132 mr = 26324 m= 3569 mr = 11637 m= 335 mr = 2352 m= 13 mr = 112 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 22139 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 27 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 7317 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) : 0.7400939 object centre at (A) : -8.534500 21.31000 35.09300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4443483E-03 4.5702696E-02 midg,1,midg; midg,igrid,midg 1.2339837E-02 1.2754331E-02 1,midg,midg; igrid,midg,midg -7.1993195E-03 2.9039790E-04 gauss-seidel spectral radius is 0.9988290 estimated iterations to convergence 231 setup time was (sec) 0.6400000 now iterating at: 09:16:45 rms-change max change #iterations 3.373820 236.1252 at 10iterations 1.651421 79.03027 at 20iterations 0.8153275 36.95440 at 30iterations 0.4018885 16.16067 at 40iterations 0.1981251 7.966152 at 50iterations 9.7552337E-02 3.831163 at 60iterations 4.8119906E-02 1.909275 at 70iterations 2.3776462E-02 0.9246740 at 80iterations 1.1684749E-02 0.4413996 at 90iterations 5.7950052E-03 0.2193804 at 100iterations 2.8507411E-03 0.1191330 at 110iterations 1.4141967E-03 5.9105873E-02 at 120iterations finished qdiffx linear iterations at : 09:16:52 total time elapsed so far: 7.140000 # loops : 120 mean,max change (kT/e) : 1.4141967E-03 5.9105873E-02 energy calculations done at 7.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.300000 DelPhi exited at 09:16:52 7.306u 0.226s 0:07.82 96.1% 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 Mon Oct 10 2011 at 09:16:52 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: 268 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1044 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: 3.330423 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): -27.20900 10.14000 ymin,ymax (A): 0.9760000 41.64400 zmin,zma (A): 11.04200 59.14400 x,y,z range (A): 37.34900 40.66800 48.10200 scale (grids/A): 3.330423 object centre (A): -8.534500 21.31000 35.09300 number of atom coordinates read : 1044 total number of charged atoms : 918 net assigned charge : 1.500003 assigned positive charge : 146.8620 centred at (gu) : 97.95657 96.38884 96.32676 assigned negative charge : -145.3620 centred at (gu) : 97.29391 96.89738 94.85033 start vw surface at 0.1200000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 97375 reading accessible surface arcs data from file ARCDAT no. of arc points read = 11491 grid for indexing accessible points = 1.400000 m= 48792 mr = 63700 m= 21066 mr = 38835 m= 6842 mr = 16943 m= 1416 mr = 5243 m= 120 mr = 922 m= 2 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.070000 number of dielectric boundary points 49927 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 7344 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) : 2.220282 object centre at (A) : -8.534500 21.31000 35.09300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7838763E-02 0.2675817 midg,1,midg; midg,igrid,midg 8.5383691E-02 0.1027129 1,midg,midg; igrid,midg,midg -2.5442977E-02 -2.5866445E-02 gauss-seidel spectral radius is 0.9992957 estimated iterations to convergence 297 setup time was (sec) 1.350000 now iterating at: 09:16:54 rms-change max change #iterations 7.522857 289.7437 at 10iterations 4.420192 126.7516 at 20iterations 2.588800 66.86634 at 30iterations 1.512219 41.30217 at 40iterations 0.8830674 21.28783 at 50iterations 0.5129447 12.93290 at 60iterations 0.2980564 7.135411 at 70iterations 0.1733104 4.137816 at 80iterations 0.1007373 2.331730 at 90iterations 5.8532204E-02 1.366514 at 100iterations 3.3977393E-02 0.7982078 at 110iterations 1.9755453E-02 0.4382005 at 120iterations 1.1425462E-02 0.2648922 at 130iterations 6.6400943E-03 0.1462693 at 140iterations 3.8532910E-03 8.4350586E-02 at 150iterations 2.2428827E-03 5.1588893E-02 at 160iterations 1.2983781E-03 2.8457642E-02 at 170iterations 7.5667613E-04 1.5191078E-02 at 180iterations finished qdiffx linear iterations at : 09:17:04 total time elapsed so far: 11.74000 # loops : 180 mean,max change (kT/e) : 7.5667613E-04 1.5191078E-02 energy calculations done at 11.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.90000 DelPhi exited at 09:17:05 11.899u 0.256s 0:12.51 97.0% 0+0k 0+0io 0pf+0w