Sat Oct 8 16:24:13 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 16:24:13 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2408 !!! WARNING: ASL 37 has a net charge of -0.1000 !!! WARNING: GLM 43 has a net charge of -0.0940 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: 0.6572875 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): -21.48500 30.33700 ymin,ymax (A): 4.002000 50.17500 zmin,zma (A): -17.04500 37.11700 x,y,z range (A): 51.82200 46.17300 54.16199 scale (grids/A): 0.6572875 object centre (A): 4.426001 27.08850 10.03600 number of atom coordinates read : 2408 total number of charged atoms : 2345 net assigned charge : 6.306002 assigned positive charge : 362.5499 centred at (gu) : 90.18188 91.10273 90.38187 assigned negative charge : -356.2448 centred at (gu) : 90.24127 90.96999 90.39926 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7171 nv = 96 ne = 84 npr = 47626 no. pairs analyzed = 47626 no. exposed pairs = 3080 no. arc points = 21331 no. surface atoms = 1048 nbur = 1360 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 423 mr = 3985 m= 6 mr = 70 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 3545 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2121 ## 196 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 8608 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6277994E-08 1.2620820E-08 midg,1,midg; midg,igrid,midg -6.2885701E-09 4.6380194E-08 1,midg,midg; igrid,midg,midg 2.3732412E-08 4.6793360E-09 gauss-seidel spectral radius is 0.9879909 estimated iterations to convergence 75 setup time was (sec) 0.6300000 now iterating at: 16:24:14 rms-change max change #iterations 0.1543862 23.63764 at 10iterations 1.5998976E-02 2.180511 at 20iterations 1.7672782E-03 0.2292194 at 30iterations 2.4377333E-04 3.6167622E-02 at 40iterations 5.6208795E-05 8.8663101E-03 at 50iterations finished qdiffx linear iterations at : 16:24:19 total time elapsed so far: 5.140000 # loops : 50 mean,max change (kT/e) : 5.6208795E-05 8.8663101E-03 energy calculations done at 5.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 5.310000 DelPhi exited at 16:24:19 5.318u 0.410s 0:06.02 95.0% 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 16:24:19 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2408 !!! WARNING: ASL 37 has a net charge of -0.1000 !!! WARNING: GLM 43 has a net charge of -0.0940 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: 1.971862 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): -21.48500 30.33700 ymin,ymax (A): 4.002000 50.17500 zmin,zma (A): -17.04500 37.11700 x,y,z range (A): 51.82200 46.17300 54.16199 scale (grids/A): 1.971862 object centre (A): 4.426001 27.08850 10.03600 number of atom coordinates read : 2408 total number of charged atoms : 2345 net assigned charge : 6.306002 assigned positive charge : 362.5499 centred at (gu) : 90.54511 93.30759 91.14500 assigned negative charge : -356.2448 centred at (gu) : 90.72350 92.90976 91.19781 start vw surface at 0.1100000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 76942 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21331 grid for indexing accessible points = 1.400000 m= 28453 mr = 53649 m= 5138 mr = 21050 m= 408 mr = 3455 m= 10 mr = 151 m= 0 mr = 0 time to grow re-entrant surface = 0.3400000 no. cavity mid-points inaccessible to solvent = 218 time to turn everything in is 0.6400000 number of dielectric boundary points 32646 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 104 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 18552 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) : 0.6572875 object centre at (A) : 4.426001 27.08850 10.03600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0503333E-02 1.5617499E-02 midg,1,midg; midg,igrid,midg -2.1571813E-03 2.9032249E-02 1,midg,midg; igrid,midg,midg 1.4495483E-02 4.8632016E-03 gauss-seidel spectral radius is 0.9987092 estimated iterations to convergence 220 setup time was (sec) 0.9600000 now iterating at: 16:24:21 rms-change max change #iterations 4.350950 165.0908 at 10iterations 2.076720 66.69801 at 20iterations 0.9895260 36.27771 at 30iterations 0.4763322 14.55739 at 40iterations 0.2275607 6.944468 at 50iterations 0.1092663 3.640859 at 60iterations 5.2358311E-02 1.683100 at 70iterations 2.5037605E-02 0.8569269 at 80iterations 1.1999650E-02 0.3662853 at 90iterations 5.7657817E-03 0.1780510 at 100iterations 2.7817949E-03 9.0337992E-02 at 110iterations 1.3429292E-03 4.1847765E-02 at 120iterations finished qdiffx linear iterations at : 16:24:32 total time elapsed so far: 12.22000 # loops : 120 mean,max change (kT/e) : 1.3429292E-03 4.1847765E-02 energy calculations done at 12.22000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.38000 DelPhi exited at 16:24:33 12.387u 0.497s 0:13.15 97.8% 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 16:24:33 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2408 !!! WARNING: ASL 37 has a net charge of -0.1000 !!! WARNING: GLM 43 has a net charge of -0.0940 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: 2.957793 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): -21.48500 30.33700 ymin,ymax (A): 4.002000 50.17500 zmin,zma (A): -17.04500 37.11700 x,y,z range (A): 51.82200 46.17300 54.16199 scale (grids/A): 2.957793 object centre (A): 4.426001 27.08850 10.03600 number of atom coordinates read : 2408 total number of charged atoms : 2345 net assigned charge : 6.306002 assigned positive charge : 362.5499 centred at (gu) : 90.81744 94.96140 91.71740 assigned negative charge : -356.2448 centred at (gu) : 91.08528 94.36457 91.79672 start vw surface at 0.1200000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 178211 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21331 grid for indexing accessible points = 1.400000 m= 90391 mr = 130408 m= 34594 mr = 73799 m= 9743 mr = 28142 m= 1667 mr = 7595 m= 181 mr = 1158 m= 8 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 859 time to turn everything in is 1.730000 number of dielectric boundary points 73604 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.880000 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) : 1.971862 object centre at (A) : 4.426001 27.08850 10.03600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.3019195E-02 0.1662627 midg,1,midg; midg,igrid,midg -4.0894281E-02 0.1676861 1,midg,midg; igrid,midg,midg 0.1392827 6.9131188E-02 gauss-seidel spectral radius is 0.9992812 estimated iterations to convergence 294 setup time was (sec) 2.100000 now iterating at: 16:24:35 rms-change max change #iterations 10.12917 491.3097 at 10iterations 5.983490 135.9851 at 20iterations 3.518421 81.48068 at 30iterations 2.067226 42.84875 at 40iterations 1.210317 24.18372 at 50iterations 0.7074581 14.90801 at 60iterations 0.4125158 7.636548 at 70iterations 0.2403819 4.512941 at 80iterations 0.1399309 2.693794 at 90iterations 8.1294090E-02 1.718252 at 100iterations 4.7241300E-02 0.8803039 at 110iterations 2.7469013E-02 0.5085402 at 120iterations 1.5925111E-02 0.2785454 at 130iterations 9.2835817E-03 0.1651344 at 140iterations 5.3817048E-03 0.1027279 at 150iterations 3.1340087E-03 5.6429386E-02 at 160iterations 1.8221494E-03 3.4724638E-02 at 170iterations 1.0627744E-03 1.9931614E-02 at 180iterations finished qdiffx linear iterations at : 16:24:54 total time elapsed so far: 20.73000 # loops : 180 mean,max change (kT/e) : 1.0627744E-03 1.9931614E-02 energy calculations done at 20.73000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.90000 DelPhi exited at 16:24:54 20.908u 0.497s 0:21.69 98.6% 0+0k 0+0io 0pf+0w