Sat Oct 8 23:21:31 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+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 Sat Oct 8 2011 at 23:21:31 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2484 !!! WARNING: HIT 84 has a net charge of 0.5140 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: 0.6396551 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): 12.84100 67.18800 ymin,ymax (A): -30.30700 25.34800 zmin,zma (A): -9.624001 32.53400 x,y,z range (A): 54.34700 55.65500 42.15800 scale (grids/A): 0.6396551 object centre (A): 40.01450 -2.479500 11.45500 number of atom coordinates read : 2484 total number of charged atoms : 2345 net assigned charge : 11.51402 assigned positive charge : 365.6610 centred at (gu) : 89.86177 90.96586 90.74911 assigned negative charge : -354.1479 centred at (gu) : 89.84451 90.99560 90.68922 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7000 nv = 96 ne = 84 npr = 49727 no. pairs analyzed = 49727 no. exposed pairs = 3335 no. arc points = 23722 no. surface atoms = 1103 nbur = 1381 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 402 mr = 3668 m= 2 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 65 time to turn everything in is 0.2900000 number of dielectric boundary points 3697 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2363 ## 235 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8294 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.8015604E-09 2.6734021E-08 midg,1,midg; midg,igrid,midg 1.6113313E-08 1.6356315E-08 1,midg,midg; igrid,midg,midg 1.5165114E-08 1.7856502E-08 gauss-seidel spectral radius is 0.9873373 estimated iterations to convergence 73 setup time was (sec) 0.5000000 now iterating at: 23:21:31 rms-change max change #iterations 0.1410503 23.51544 at 10iterations 1.3956702E-02 1.992321 at 20iterations 1.4969732E-03 0.2296791 at 30iterations 2.5681558E-04 4.7405243E-02 at 40iterations 7.9943442E-05 1.6851425E-02 at 50iterations finished qdiffx linear iterations at : 23:21:34 total time elapsed so far: 2.880000 # loops : 50 mean,max change (kT/e) : 7.9943442E-05 1.6851425E-02 energy calculations done at 2.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.050000 DelPhi exited at 23:21:34 3.053u 0.159s 0:03.49 91.6% 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 Sat Oct 8 2011 at 23:21:34 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2484 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.918965 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): 12.84100 67.18800 ymin,ymax (A): -30.30700 25.34800 zmin,zma (A): -9.624001 32.53400 x,y,z range (A): 54.34700 55.65500 42.15800 scale (grids/A): 1.918965 object centre (A): 40.01450 -2.479500 11.45500 number of atom coordinates read : 2484 total number of charged atoms : 2345 net assigned charge : 11.51402 assigned positive charge : 365.6610 centred at (gu) : 89.58481 92.89724 92.24689 assigned negative charge : -354.1479 centred at (gu) : 89.53347 92.98667 92.06778 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 75363 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23722 grid for indexing accessible points = 1.400000 m= 26808 mr = 50745 m= 4116 mr = 19132 m= 269 mr = 2427 m= 3 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 821 time to turn everything in is 0.5200000 number of dielectric boundary points 34164 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 180 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 18479 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) : 0.6396551 object centre at (A) : 40.01450 -2.479500 11.45500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5421226E-03 3.4030665E-02 midg,1,midg; midg,igrid,midg 4.6280365E-02 2.9128179E-02 1,midg,midg; igrid,midg,midg 4.9557805E-02 5.5747103E-02 gauss-seidel spectral radius is 0.9986562 estimated iterations to convergence 216 setup time was (sec) 0.7800000 now iterating at: 23:21:35 rms-change max change #iterations 4.136868 164.5278 at 10iterations 1.944601 70.01260 at 20iterations 0.9158820 30.34452 at 30iterations 0.4282404 13.04871 at 40iterations 0.2023604 7.238945 at 50iterations 9.5117882E-02 2.887583 at 60iterations 4.4692926E-02 1.436775 at 70iterations 2.0983433E-02 0.7127876 at 80iterations 9.9520078E-03 0.3045998 at 90iterations 4.7029732E-03 0.1399794 at 100iterations 2.2389782E-03 6.7612648E-02 at 110iterations 1.0786338E-03 3.5634995E-02 at 120iterations finished qdiffx linear iterations at : 23:21:41 total time elapsed so far: 6.660000 # loops : 120 mean,max change (kT/e) : 1.0786338E-03 3.5634995E-02 energy calculations done at 6.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.840000 DelPhi exited at 23:21:42 6.845u 0.167s 0:07.34 95.3% 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 Sat Oct 8 2011 at 23:21:42 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: 290 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2484 !!! WARNING: HIT 84 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.878448 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): 12.84100 67.18800 ymin,ymax (A): -30.30700 25.34800 zmin,zma (A): -9.624001 32.53400 x,y,z range (A): 54.34700 55.65500 42.15800 scale (grids/A): 2.878448 object centre (A): 40.01450 -2.479500 11.45500 number of atom coordinates read : 2484 total number of charged atoms : 2345 net assigned charge : 11.51402 assigned positive charge : 365.6610 centred at (gu) : 89.37707 94.34585 93.37028 assigned negative charge : -354.1479 centred at (gu) : 89.30013 94.48005 93.10162 start vw surface at 0.1200000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 174106 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23722 grid for indexing accessible points = 1.400000 m= 86211 mr = 123331 m= 30891 mr = 69212 m= 7508 mr = 24105 m= 1194 mr = 5456 m= 82 mr = 764 m= 2 mr = 48 m= 0 mr = 0 time to grow re-entrant surface = 0.7700000 no. cavity mid-points inaccessible to solvent = 2734 time to turn everything in is 1.280000 number of dielectric boundary points 77078 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 18760 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) : 1.918965 object centre at (A) : 40.01450 -2.479500 11.45500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6717344E-02 0.3646844 midg,1,midg; midg,igrid,midg 0.5948533 0.3751007 1,midg,midg; igrid,midg,midg 0.5066569 0.5817363 gauss-seidel spectral radius is 0.9992734 estimated iterations to convergence 293 setup time was (sec) 1.560000 now iterating at: 23:21:43 rms-change max change #iterations 9.802757 380.7795 at 10iterations 5.817597 133.0563 at 20iterations 3.408905 77.14552 at 30iterations 1.991495 42.95284 at 40iterations 1.165883 25.83957 at 50iterations 0.6798660 13.06979 at 60iterations 0.3954905 7.749221 at 70iterations 0.2296230 4.338385 at 80iterations 0.1333220 2.395761 at 90iterations 7.6976322E-02 1.609248 at 100iterations 4.4722594E-02 0.8863411 at 110iterations 2.5831880E-02 0.4884796 at 120iterations 1.4953897E-02 0.2938986 at 130iterations 8.6695859E-03 0.1603031 at 140iterations 5.0227400E-03 9.5878601E-02 at 150iterations 2.9245308E-03 6.2832832E-02 at 160iterations 1.7089616E-03 3.2243729E-02 at 170iterations 1.0107685E-03 2.3429871E-02 at 180iterations finished qdiffx linear iterations at : 23:21:53 total time elapsed so far: 11.01000 # loops : 180 mean,max change (kT/e) : 1.0107685E-03 2.3429871E-02 energy calculations done at 11.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.19000 DelPhi exited at 23:21:53 11.189u 0.185s 0:11.64 97.5% 0+0k 0+0io 0pf+0w