Tue Oct 11 01:45:54 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 Tue Oct 11 2011 at 01:45:54 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 = 2698 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: 0.5645954 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): 18.24600 81.30000 ymin,ymax (A): -10.72900 45.23100 zmin,zma (A): -7.754000 35.60400 x,y,z range (A): 63.05400 55.96000 43.35800 scale (grids/A): 0.5645954 object centre (A): 49.77300 17.25100 13.92500 number of atom coordinates read : 2698 total number of charged atoms : 2555 net assigned charge : 4.500015 assigned positive charge : 408.4216 centred at (gu) : 87.53798 89.48387 89.90133 assigned negative charge : -403.9224 centred at (gu) : 87.75549 89.63352 90.03632 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5578 nv = 96 ne = 84 npr = 53704 no. pairs analyzed = 53704 no. exposed pairs = 3287 no. arc points = 23292 no. surface atoms = 1105 nbur = 1593 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 229 mr = 3006 m= 0 mr = 16 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 34 time to turn everything in is 0.3400000 number of dielectric boundary points 2785 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2276 ## 265 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 7158 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0978861E-09 -1.1014859E-09 midg,1,midg; midg,igrid,midg 2.5097080E-09 -1.1499688E-09 1,midg,midg; igrid,midg,midg 5.4520672E-09 -1.1746984E-09 gauss-seidel spectral radius is 0.9837906 estimated iterations to convergence 65 setup time was (sec) 0.5800000 now iterating at: 01:45:55 rms-change max change #iterations 8.5117064E-02 16.86770 at 10iterations 7.2612455E-03 1.249966 at 20iterations 9.9344004E-04 0.2612457 at 30iterations 2.3083259E-04 6.2625885E-02 at 40iterations 5.6233777E-05 1.5506744E-02 at 50iterations finished qdiffx linear iterations at : 01:45:58 total time elapsed so far: 3.850000 # loops : 50 mean,max change (kT/e) : 5.6233777E-05 1.5506744E-02 energy calculations done at 3.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.020000 DelPhi exited at 01:45:58 4.027u 0.301s 0:04.62 93.5% 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 Tue Oct 11 2011 at 01:45:58 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 = 2698 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: 1.693786 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): 18.24600 81.30000 ymin,ymax (A): -10.72900 45.23100 zmin,zma (A): -7.754000 35.60400 x,y,z range (A): 63.05400 55.96000 43.35800 scale (grids/A): 1.693786 object centre (A): 49.77300 17.25100 13.92500 number of atom coordinates read : 2698 total number of charged atoms : 2555 net assigned charge : 4.500015 assigned positive charge : 408.4216 centred at (gu) : 82.61320 88.45105 89.70320 assigned negative charge : -403.9224 centred at (gu) : 83.26588 88.90016 90.10863 start vw surface at 0.1600000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 61834 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23292 grid for indexing accessible points = 1.400000 m= 19670 mr = 42530 m= 2395 mr = 14128 m= 57 mr = 1353 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 2348 time to turn everything in is 0.5600000 number of dielectric boundary points 25943 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 227 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 19735 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) : 0.5645954 object centre at (A) : 49.77300 17.25100 13.92500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4127284E-02 1.5711241E-03 midg,1,midg; midg,igrid,midg 1.6433744E-02 -2.5589095E-02 1,midg,midg; igrid,midg,midg -2.1317301E-03 -1.8876684E-03 gauss-seidel spectral radius is 0.9982828 estimated iterations to convergence 192 setup time was (sec) 0.8400000 now iterating at: 01:45:59 rms-change max change #iterations 3.391127 159.3322 at 10iterations 1.440449 53.49687 at 20iterations 0.6159130 22.31321 at 30iterations 0.2632518 9.863964 at 40iterations 0.1128042 4.178104 at 50iterations 4.8351120E-02 1.703713 at 60iterations 2.0793149E-02 0.7526512 at 70iterations 8.9882882E-03 0.3419991 at 80iterations 3.9358423E-03 0.1543694 at 90iterations 1.7605944E-03 7.6629639E-02 at 100iterations 8.2106469E-04 3.6201477E-02 at 110iterations 3.9892225E-04 1.9432068E-02 at 120iterations finished qdiffx linear iterations at : 01:46:08 total time elapsed so far: 8.920000 # loops : 120 mean,max change (kT/e) : 3.9892225E-04 1.9432068E-02 energy calculations done at 8.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.100000 DelPhi exited at 01:46:08 9.098u 0.306s 0:09.95 94.3% 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 Tue Oct 11 2011 at 01:46:08 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 = 2698 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: 2.540679 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): 18.24600 81.30000 ymin,ymax (A): -10.72900 45.23100 zmin,zma (A): -7.754000 35.60400 x,y,z range (A): 63.05400 55.96000 43.35800 scale (grids/A): 2.540679 object centre (A): 49.77300 17.25100 13.92500 number of atom coordinates read : 2698 total number of charged atoms : 2555 net assigned charge : 4.500015 assigned positive charge : 408.4216 centred at (gu) : 78.91965 87.67640 89.55469 assigned negative charge : -403.9224 centred at (gu) : 79.89879 88.35021 90.16287 start vw surface at 0.1700000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 143576 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23292 grid for indexing accessible points = 1.400000 m= 67491 mr = 103649 m= 20540 mr = 54592 m= 3859 mr = 16054 m= 274 mr = 2780 m= 3 mr = 129 m= 0 mr = 0 time to grow re-entrant surface = 0.7800000 no. cavity mid-points inaccessible to solvent = 7719 time to turn everything in is 1.340000 number of dielectric boundary points 58539 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.490000 number of grid points assigned charge 20428 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) : 1.693786 object centre at (A) : 49.77300 17.25100 13.92500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1657223 2.4808951E-02 midg,1,midg; midg,igrid,midg 0.2167076 -0.4797127 1,midg,midg; igrid,midg,midg -4.0434942E-02 7.8392521E-02 gauss-seidel spectral radius is 0.9991549 estimated iterations to convergence 272 setup time was (sec) 1.660000 now iterating at: 01:46:10 rms-change max change #iterations 8.440428 283.8348 at 10iterations 4.665343 106.1887 at 20iterations 2.590132 53.98567 at 30iterations 1.435725 30.64700 at 40iterations 0.7941504 17.21286 at 50iterations 0.4387399 8.945914 at 60iterations 0.2423552 4.801979 at 70iterations 0.1339397 2.703407 at 80iterations 7.4014761E-02 1.604653 at 90iterations 4.0987588E-02 0.8857231 at 100iterations 2.2750689E-02 0.4956741 at 110iterations 1.2625180E-02 0.2577267 at 120iterations 7.0714252E-03 0.1528244 at 130iterations 3.9992342E-03 8.8603973E-02 at 140iterations 2.3035244E-03 5.7796478E-02 at 150iterations 1.3593249E-03 3.5205841E-02 at 160iterations 8.3659764E-04 2.3227692E-02 at 170iterations 5.3416123E-04 1.4778137E-02 at 180iterations finished qdiffx linear iterations at : 01:46:23 total time elapsed so far: 14.71000 # loops : 180 mean,max change (kT/e) : 5.3416123E-04 1.4778137E-02 energy calculations done at 14.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.89000 DelPhi exited at 01:46:24 14.891u 0.302s 0:15.46 98.2% 0+0k 0+0io 0pf+0w