Sun Oct 9 06:01:52 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 Sun Oct 9 2011 at 06:01:53 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: 233 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1747 !!! WARNING: HIZ 132 has a net charge of 0.2000 !!! WARNING: HIZ 136 has a net charge of 0.2000 !!! WARNING: ZN1 185 has a net charge of 1.4000 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: 0.6867151 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): 15.54500 67.38600 ymin,ymax (A): 26.67400 77.60201 zmin,zma (A): 47.75000 89.03699 x,y,z range (A): 51.84100 50.92801 41.28699 scale (grids/A): 0.6867151 object centre (A): 41.46550 52.13800 68.39349 number of atom coordinates read : 1747 total number of charged atoms : 1607 net assigned charge : -5.199989 assigned positive charge : 265.4792 centred at (gu) : 90.70592 91.45007 90.57199 assigned negative charge : -270.6792 centred at (gu) : 90.81585 91.91293 90.63905 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5665 nv = 96 ne = 84 npr = 35683 no. pairs analyzed = 35683 no. exposed pairs = 2236 no. arc points = 15798 no. surface atoms = 755 nbur = 992 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 354 mr = 3079 m= 2 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 27 time to turn everything in is 0.2300000 number of dielectric boundary points 2875 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1468 ## 121 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 6310 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.5599734E-09 -4.6636551E-08 midg,1,midg; midg,igrid,midg 6.9274655E-08 -2.0539510E-07 1,midg,midg; igrid,midg,midg 4.2186756E-09 -6.1283792E-08 gauss-seidel spectral radius is 0.9889283 estimated iterations to convergence 77 setup time was (sec) 0.4400000 now iterating at: 06:01:53 rms-change max change #iterations 0.1635160 30.56750 at 10iterations 1.9099552E-02 2.987085 at 20iterations 2.1349106E-03 0.3267457 at 30iterations 2.4832992E-04 3.6979198E-02 at 40iterations 2.7885466E-05 4.0464401E-03 at 50iterations finished qdiffx linear iterations at : 06:01:55 total time elapsed so far: 2.830000 # loops : 50 mean,max change (kT/e) : 2.7885466E-05 4.0464401E-03 energy calculations done at 2.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.000000 DelPhi exited at 06:01:56 3.007u 0.146s 0:03.43 91.5% 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 06:01:56 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: 233 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1747 !!! WARNING: HIZ 132 has a net charge of 0.2000 !!! WARNING: HIZ 136 has a net charge of 0.2000 !!! WARNING: ZN1 185 has a net charge of 1.4000 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: 2.060145 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): 15.54500 67.38600 ymin,ymax (A): 26.67400 77.60201 zmin,zma (A): 47.75000 89.03699 x,y,z range (A): 51.84100 50.92801 41.28699 scale (grids/A): 2.060145 object centre (A): 41.46550 52.13800 68.39349 number of atom coordinates read : 1747 total number of charged atoms : 1607 net assigned charge : -5.199989 assigned positive charge : 265.4792 centred at (gu) : 92.11794 94.35030 91.71609 assigned negative charge : -270.6792 centred at (gu) : 92.44771 95.73882 91.91726 start vw surface at 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 59716 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15798 grid for indexing accessible points = 1.400000 m= 22797 mr = 40413 m= 4368 mr = 17309 m= 360 mr = 3029 m= 8 mr = 213 m= 0 mr = 4 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 761 time to turn everything in is 0.4400000 number of dielectric boundary points 26281 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 63 iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 12755 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) : 0.6867151 object centre at (A) : 41.46550 52.13800 68.39349 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.4795425E-03 -2.9481644E-02 midg,1,midg; midg,igrid,midg 6.8655908E-02 -7.1638994E-02 1,midg,midg; igrid,midg,midg -1.9938815E-02 -5.3558715E-02 gauss-seidel spectral radius is 0.9987378 estimated iterations to convergence 223 setup time was (sec) 0.7000000 now iterating at: 06:01:57 rms-change max change #iterations 4.094084 238.6616 at 10iterations 1.974513 73.37335 at 20iterations 0.9527217 30.77088 at 30iterations 0.4584814 15.36172 at 40iterations 0.2211402 7.305603 at 50iterations 0.1065049 3.634205 at 60iterations 5.1466119E-02 1.885221 at 70iterations 2.4853107E-02 0.7776642 at 80iterations 1.1970096E-02 0.4302464 at 90iterations 5.7675983E-03 0.1914158 at 100iterations 2.7850529E-03 9.5970154E-02 at 110iterations 1.3442342E-03 4.5499802E-02 at 120iterations finished qdiffx linear iterations at : 06:02:03 total time elapsed so far: 6.540000 # loops : 120 mean,max change (kT/e) : 1.3442342E-03 4.5499802E-02 energy calculations done at 6.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.710000 DelPhi exited at 06:02:03 6.717u 0.170s 0:07.15 96.2% 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 06:02:03 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: 233 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1747 !!! WARNING: HIZ 132 has a net charge of 0.2000 !!! WARNING: HIZ 136 has a net charge of 0.2000 !!! WARNING: ZN1 185 has a net charge of 1.4000 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: 3.090218 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): 15.54500 67.38600 ymin,ymax (A): 26.67400 77.60201 zmin,zma (A): 47.75000 89.03699 x,y,z range (A): 51.84100 50.92801 41.28699 scale (grids/A): 3.090218 object centre (A): 41.46550 52.13800 68.39349 number of atom coordinates read : 1747 total number of charged atoms : 1607 net assigned charge : -5.199989 assigned positive charge : 265.4792 centred at (gu) : 93.17696 96.52551 92.57428 assigned negative charge : -270.6792 centred at (gu) : 93.67165 98.60831 92.87603 start vw surface at 0.1200000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 137419 reading accessible surface arcs data from file ARCDAT no. of arc points read = 15798 grid for indexing accessible points = 1.400000 m= 71250 mr = 97583 m= 29029 mr = 58921 m= 8229 mr = 24092 m= 1547 mr = 6574 m= 188 mr = 1207 m= 9 mr = 140 m= 0 mr = 6 time to grow re-entrant surface = 0.6300001 no. cavity mid-points inaccessible to solvent = 2432 time to turn everything in is 1.330000 number of dielectric boundary points 59148 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 12856 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) : 2.060145 object centre at (A) : 41.46550 52.13800 68.39349 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1871364 -0.2213165 midg,1,midg; midg,igrid,midg 0.6223924 -0.5289715 1,midg,midg; igrid,midg,midg -0.2166411 -0.6010103 gauss-seidel spectral radius is 0.9992738 estimated iterations to convergence 293 setup time was (sec) 1.590000 now iterating at: 06:02:05 rms-change max change #iterations 9.254795 395.3256 at 10iterations 5.349492 124.7908 at 20iterations 3.098897 67.86668 at 30iterations 1.790967 39.20571 at 40iterations 1.035144 20.06466 at 50iterations 0.5978696 12.05487 at 60iterations 0.3459615 6.789871 at 70iterations 0.1992482 3.932918 at 80iterations 0.1149622 2.401262 at 90iterations 6.6396624E-02 1.404632 at 100iterations 3.8334604E-02 0.7683592 at 110iterations 2.2089858E-02 0.4860954 at 120iterations 1.2745986E-02 0.2545509 at 130iterations 7.3614162E-03 0.1347008 at 140iterations 4.2447345E-03 8.7532043E-02 at 150iterations 2.4536357E-03 5.1321507E-02 at 160iterations 1.4228437E-03 3.1078339E-02 at 170iterations 8.2519348E-04 2.0042419E-02 at 180iterations finished qdiffx linear iterations at : 06:02:14 total time elapsed so far: 10.76000 # loops : 180 mean,max change (kT/e) : 8.2519348E-04 2.0042419E-02 energy calculations done at 10.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.93000 DelPhi exited at 06:02:15 10.931u 0.204s 0:11.39 97.7% 0+0k 0+0io 0pf+0w