Mon Oct 10 14:18:34 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 14:18:34 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: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1159 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: 0.8436418 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): -0.8750000 41.32300 ymin,ymax (A): -0.1040000 36.91600 zmin,zma (A): 7.131999 45.01200 x,y,z range (A): 42.19800 37.02000 37.88000 scale (grids/A): 0.8436418 object centre (A): 20.22400 18.40600 26.07200 number of atom coordinates read : 1159 total number of charged atoms : 1031 net assigned charge : 2.000003 assigned positive charge : 170.8011 centred at (gu) : 90.90744 90.24077 89.18541 assigned negative charge : -168.8010 centred at (gu) : 90.95016 90.32568 89.34751 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5783 nv = 96 ne = 84 npr = 22813 no. pairs analyzed = 22813 no. exposed pairs = 1487 no. arc points = 10832 no. surface atoms = 503 nbur = 656 mkacc time = 4.9999997E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 487 mr = 3169 m= 8 mr = 136 m= 0 mr = 0 time to grow re-entrant surface = 6.0000002E-02 no. cavity mid-points inaccessible to solvent = 70 time to turn everything in is 0.2300000 number of dielectric boundary points 2973 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 670 ## 71 charges are in solution ## iepsmp to db, and charging done at 0.3300000 number of grid points assigned charge 5201 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.1699673E-07 -2.6778653E-07 midg,1,midg; midg,igrid,midg 5.1974723E-07 -4.2897693E-08 1,midg,midg; igrid,midg,midg 3.4338660E-07 1.2018005E-07 gauss-seidel spectral radius is 0.9925663 estimated iterations to convergence 94 setup time was (sec) 0.4700000 now iterating at: 14:18:34 rms-change max change #iterations 0.2958168 52.06752 at 10iterations 4.9486101E-02 6.964737 at 20iterations 8.5300868E-03 1.128317 at 30iterations 1.4346115E-03 0.2196484 at 40iterations 2.4399821E-04 4.4700623E-02 at 50iterations finished qdiffx linear iterations at : 14:18:37 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 2.4399821E-04 4.4700623E-02 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 14:18:38 3.437u 0.174s 0:03.99 90.2% 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 Mon Oct 10 2011 at 14:18:38 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: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1159 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.530926 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): -0.8750000 41.32300 ymin,ymax (A): -0.1040000 36.91600 zmin,zma (A): 7.131999 45.01200 x,y,z range (A): 42.19800 37.02000 37.88000 scale (grids/A): 2.530926 object centre (A): 20.22400 18.40600 26.07200 number of atom coordinates read : 1159 total number of charged atoms : 1031 net assigned charge : 2.000003 assigned positive charge : 170.8011 centred at (gu) : 92.72224 90.72237 87.55630 assigned negative charge : -168.8010 centred at (gu) : 92.85049 90.97713 88.04252 start vw surface at 0.1100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 59286 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10832 grid for indexing accessible points = 1.400000 m= 24507 mr = 39641 m= 6226 mr = 18900 m= 917 mr = 4604 m= 52 mr = 591 m= 3 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 2167 time to turn everything in is 0.4900000 number of dielectric boundary points 27235 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 8238 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) : 0.8436418 object centre at (A) : 20.22400 18.40600 26.07200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.2531760E-02 -1.0628372E-02 midg,1,midg; midg,igrid,midg 2.6913820E-02 -1.1359775E-02 1,midg,midg; igrid,midg,midg 9.9390075E-03 1.2861200E-02 gauss-seidel spectral radius is 0.9990468 estimated iterations to convergence 256 setup time was (sec) 0.8000000 now iterating at: 14:18:39 rms-change max change #iterations 4.581802 279.2083 at 10iterations 2.425003 118.8950 at 20iterations 1.280770 43.37069 at 30iterations 0.6772122 22.44019 at 40iterations 0.3579172 11.35914 at 50iterations 0.1903077 6.417154 at 60iterations 0.1008661 3.359169 at 70iterations 5.3478874E-02 1.666449 at 80iterations 2.8218718E-02 0.9005089 at 90iterations 1.5002459E-02 0.5038033 at 100iterations 7.9492480E-03 0.2566986 at 110iterations 4.2179124E-03 0.1349554 at 120iterations finished qdiffx linear iterations at : 14:18:46 total time elapsed so far: 7.620000 # loops : 120 mean,max change (kT/e) : 4.2179124E-03 0.1349554 energy calculations done at 7.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 14:18:46 7.812u 0.213s 0:08.43 95.1% 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 14:18:46 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: 227 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1159 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.796388 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): -0.8750000 41.32300 ymin,ymax (A): -0.1040000 36.91600 zmin,zma (A): 7.131999 45.01200 x,y,z range (A): 42.19800 37.02000 37.88000 scale (grids/A): 3.796388 object centre (A): 20.22400 18.40600 26.07200 number of atom coordinates read : 1159 total number of charged atoms : 1031 net assigned charge : 2.000003 assigned positive charge : 170.8011 centred at (gu) : 94.08338 91.08363 86.33441 assigned negative charge : -168.8010 centred at (gu) : 94.27572 91.46574 87.06384 start vw surface at 0.1200000 fill in re-entrant regions at 0.7300000 boundary points on vw surface= 136184 reading accessible surface arcs data from file ARCDAT no. of arc points read = 10832 grid for indexing accessible points = 1.400000 m= 72780 mr = 95325 m= 34110 mr = 60648 m= 12487 mr = 28872 m= 3602 mr = 10241 m= 653 mr = 2937 m= 52 mr = 462 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.7399999 no. cavity mid-points inaccessible to solvent = 7723 time to turn everything in is 1.580000 number of dielectric boundary points 61361 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.720000 number of grid points assigned charge 8248 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) : 2.530926 object centre at (A) : 20.22400 18.40600 26.07200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5205330 -5.9753790E-02 midg,1,midg; midg,igrid,midg 0.1877240 -4.5917157E-02 1,midg,midg; igrid,midg,midg 2.2954438E-02 -9.6015148E-03 gauss-seidel spectral radius is 0.9993346 estimated iterations to convergence 306 setup time was (sec) 1.910000 now iterating at: 14:18:48 rms-change max change #iterations 9.372085 247.2882 at 10iterations 5.531199 132.5946 at 20iterations 3.265433 61.77242 at 30iterations 1.925779 37.86646 at 40iterations 1.136125 26.84830 at 50iterations 0.6685137 12.81764 at 60iterations 0.3960807 7.539185 at 70iterations 0.2323592 4.252208 at 80iterations 0.1371481 2.415161 at 90iterations 8.0962218E-02 1.442081 at 100iterations 4.7702234E-02 0.8595390 at 110iterations 2.8133834E-02 0.5127964 at 120iterations 1.6630145E-02 0.2939625 at 130iterations 9.8344637E-03 0.1913376 at 140iterations 5.8114687E-03 0.1061611 at 150iterations 3.4294052E-03 6.7775726E-02 at 160iterations 2.0203723E-03 3.6918640E-02 at 170iterations 1.1936665E-03 2.0700455E-02 at 180iterations finished qdiffx linear iterations at : 14:18:59 total time elapsed so far: 12.71000 # loops : 180 mean,max change (kT/e) : 1.1936665E-03 2.0700455E-02 energy calculations done at 12.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.90000 DelPhi exited at 14:19:00 12.904u 0.214s 0:14.02 93.5% 0+0k 0+0io 0pf+0w