Mon Oct 10 09:26:05 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 Mon Oct 10 2011 at 09:26:05 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 = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6565359 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): -5.751000 35.01000 ymin,ymax (A): -3.112000 50.46700 zmin,zma (A): -23.16600 31.05800 x,y,z range (A): 40.76100 53.57900 54.22400 scale (grids/A): 0.6565359 object centre (A): 14.62950 23.67750 3.946000 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 5.000007 assigned positive charge : 287.8260 centred at (gu) : 90.89613 92.25396 89.80813 assigned negative charge : -282.8263 centred at (gu) : 90.95219 92.32841 89.76920 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 5905 nv = 96 ne = 84 npr = 39931 no. pairs analyzed = 39931 no. exposed pairs = 2413 no. arc points = 17127 no. surface atoms = 823 nbur = 1139 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 327 mr = 3352 m= 4 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 23 time to turn everything in is 0.2400000 number of dielectric boundary points 2838 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1696 ## 183 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 6711 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.9688362E-09 1.6260644E-08 midg,1,midg; midg,igrid,midg 1.3575180E-08 2.7590656E-09 1,midg,midg; igrid,midg,midg 1.5922557E-08 5.2418199E-09 gauss-seidel spectral radius is 0.9879211 estimated iterations to convergence 74 setup time was (sec) 0.4500000 now iterating at: 09:26:06 rms-change max change #iterations 0.1369218 19.40817 at 10iterations 1.4258090E-02 2.213589 at 20iterations 1.4825070E-03 0.2406383 at 30iterations 1.5643754E-04 2.4603844E-02 at 40iterations 1.6404467E-05 2.6054382E-03 at 50iterations finished qdiffx linear iterations at : 09:26:08 total time elapsed so far: 3.020000 # loops : 50 mean,max change (kT/e) : 1.6404467E-05 2.6054382E-03 energy calculations done at 3.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.190000 DelPhi exited at 09:26:09 3.191u 0.209s 0:03.77 89.9% 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 09:26:09 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 = 1962 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.969608 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): -5.751000 35.01000 ymin,ymax (A): -3.112000 50.46700 zmin,zma (A): -23.16600 31.05800 x,y,z range (A): 40.76100 53.57900 54.22400 scale (grids/A): 1.969608 object centre (A): 14.62950 23.67750 3.946000 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 5.000007 assigned positive charge : 287.8260 centred at (gu) : 92.68817 96.76205 89.42443 assigned negative charge : -282.8263 centred at (gu) : 92.85677 96.98556 89.30767 start vw surface at 0.1200000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 62602 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17127 grid for indexing accessible points = 1.400000 m= 25070 mr = 43541 m= 4437 mr = 19552 m= 275 mr = 3012 m= 2 mr = 115 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 1545 time to turn everything in is 0.4500000 number of dielectric boundary points 26166 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 112 iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 14467 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) : 0.6565359 object centre at (A) : 14.62950 23.67750 3.946000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8802592E-02 1.6547799E-02 midg,1,midg; midg,igrid,midg 4.1582540E-02 1.2070447E-02 1,midg,midg; igrid,midg,midg 7.8605581E-03 -6.9418544E-04 gauss-seidel spectral radius is 0.9986455 estimated iterations to convergence 215 setup time was (sec) 0.7400000 now iterating at: 09:26:10 rms-change max change #iterations 3.763227 180.4924 at 10iterations 1.770555 71.10686 at 20iterations 0.8306292 27.97721 at 30iterations 0.3890655 13.97709 at 40iterations 0.1834488 6.507172 at 50iterations 8.5659117E-02 3.191139 at 60iterations 4.0303878E-02 1.385496 at 70iterations 1.8904287E-02 0.7478099 at 80iterations 8.8829752E-03 0.3020782 at 90iterations 4.1651810E-03 0.1353266 at 100iterations 1.9604648E-03 6.5126419E-02 at 110iterations 9.2273008E-04 3.0962646E-02 at 120iterations finished qdiffx linear iterations at : 09:26:16 total time elapsed so far: 7.080000 # loops : 120 mean,max change (kT/e) : 9.2273008E-04 3.0962646E-02 energy calculations done at 7.080000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.250000 DelPhi exited at 09:26:17 7.251u 0.238s 0:07.78 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 09:26:17 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 = 1962 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: 2.954411 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): -5.751000 35.01000 ymin,ymax (A): -3.112000 50.46700 zmin,zma (A): -23.16600 31.05800 x,y,z range (A): 40.76100 53.57900 54.22400 scale (grids/A): 2.954411 object centre (A): 14.62950 23.67750 3.946000 number of atom coordinates read : 1962 total number of charged atoms : 1830 net assigned charge : 5.000007 assigned positive charge : 287.8260 centred at (gu) : 94.03236 100.1430 89.13662 assigned negative charge : -282.8263 centred at (gu) : 94.28524 100.4783 88.96157 start vw surface at 0.1100000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 144311 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17127 grid for indexing accessible points = 1.400000 m= 77853 mr = 104808 m= 32000 mr = 65314 m= 8146 mr = 27122 m= 1170 mr = 6461 m= 62 mr = 811 m= 0 mr = 32 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 5342 time to turn everything in is 1.150000 number of dielectric boundary points 58994 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.280000 number of grid points assigned charge 14640 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) : 1.969608 object centre at (A) : 14.62950 23.67750 3.946000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.9052654 7.5086810E-02 midg,1,midg; midg,igrid,midg 0.3716170 1.1052022E-02 1,midg,midg; igrid,midg,midg 3.9787263E-02 -3.4118276E-03 gauss-seidel spectral radius is 0.9992495 estimated iterations to convergence 288 setup time was (sec) 1.460000 now iterating at: 09:26:18 rms-change max change #iterations 8.783992 521.7380 at 10iterations 5.075721 155.7308 at 20iterations 2.903364 61.09487 at 30iterations 1.667910 34.43162 at 40iterations 0.9593425 19.38567 at 50iterations 0.5475835 10.67902 at 60iterations 0.3134604 6.809513 at 70iterations 0.1791832 3.570335 at 80iterations 0.1022704 1.900951 at 90iterations 5.8533214E-02 1.117020 at 100iterations 3.3431284E-02 0.7404585 at 110iterations 1.9131463E-02 0.3747864 at 120iterations 1.0915975E-02 0.2075195 at 130iterations 6.2482795E-03 0.1218863 at 140iterations 3.5675250E-03 7.0744276E-02 at 150iterations 2.0344257E-03 4.4235229E-02 at 160iterations 1.1626822E-03 2.2837639E-02 at 170iterations 6.6402863E-04 1.3063431E-02 at 180iterations finished qdiffx linear iterations at : 09:26:29 total time elapsed so far: 11.89000 # loops : 180 mean,max change (kT/e) : 6.6402863E-04 1.3063431E-02 energy calculations done at 11.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.07000 DelPhi exited at 09:26:29 12.068u 0.338s 0:12.80 96.7% 0+0k 0+0io 0pf+0w