Mon Oct 10 18:46:27 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 Mon Oct 10 2011 at 18:46:27 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2417 !!! WARNING: HIR 257 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.7001395 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): -14.58300 31.95400 ymin,ymax (A): -6.962000 40.17600 zmin,zma (A): 34.89500 85.74200 x,y,z range (A): 46.53700 47.13800 50.84701 scale (grids/A): 0.7001395 object centre (A): 8.685501 16.60700 60.31850 number of atom coordinates read : 2417 total number of charged atoms : 2280 net assigned charge : 1.014006 assigned positive charge : 362.0128 centred at (gu) : 89.32445 91.65599 88.94775 assigned negative charge : -360.9995 centred at (gu) : 89.46793 91.65846 88.91131 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8384 nv = 96 ne = 84 npr = 48206 no. pairs analyzed = 48206 no. exposed pairs = 3125 no. arc points = 21621 no. surface atoms = 1048 nbur = 1369 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 611 mr = 4738 m= 7 mr = 116 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2900000 number of dielectric boundary points 4148 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1934 ## 156 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 9089 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3440250E-08 1.9888178E-08 midg,1,midg; midg,igrid,midg 5.9280305E-09 7.8143616E-09 1,midg,midg; igrid,midg,midg 8.6223736E-08 -5.5342422E-08 gauss-seidel spectral radius is 0.9894125 estimated iterations to convergence 79 setup time was (sec) 0.5000000 now iterating at: 18:46:28 rms-change max change #iterations 0.2035782 24.97953 at 10iterations 2.4497762E-02 3.481163 at 20iterations 3.1586264E-03 0.4011288 at 30iterations 4.9927074E-04 7.2975159E-02 at 40iterations 1.3994184E-04 2.1340370E-02 at 50iterations finished qdiffx linear iterations at : 18:46:30 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 1.3994184E-04 2.1340370E-02 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.050000 DelPhi exited at 18:46:31 3.057u 0.176s 0:03.65 88.2% 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 18:46:31 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2417 !!! WARNING: HIR 257 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: 2.100419 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): -14.58300 31.95400 ymin,ymax (A): -6.962000 40.17600 zmin,zma (A): 34.89500 85.74200 x,y,z range (A): 46.53700 47.13800 50.84701 scale (grids/A): 2.100419 object centre (A): 8.685501 16.60700 60.31850 number of atom coordinates read : 2417 total number of charged atoms : 2280 net assigned charge : 1.014006 assigned positive charge : 362.0128 centred at (gu) : 87.97249 94.96725 86.84245 assigned negative charge : -360.9995 centred at (gu) : 88.40367 94.97522 86.73344 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 88770 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21621 grid for indexing accessible points = 1.400000 m= 36137 mr = 62206 m= 7458 mr = 27299 m= 744 mr = 5036 m= 19 mr = 359 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6000000 number of dielectric boundary points 38228 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 83 iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 18090 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) : 0.7001395 object centre at (A) : 8.685501 16.60700 60.31850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.6891655E-03 2.7521461E-02 midg,1,midg; midg,igrid,midg -1.0358961E-03 -1.0629321E-02 1,midg,midg; igrid,midg,midg 2.9992364E-02 -1.6660852E-02 gauss-seidel spectral radius is 0.9988534 estimated iterations to convergence 234 setup time was (sec) 0.8700000 now iterating at: 18:46:32 rms-change max change #iterations 4.958656 212.9035 at 10iterations 2.464919 70.11652 at 20iterations 1.235029 35.86951 at 30iterations 0.6167164 17.99379 at 40iterations 0.3085710 9.151784 at 50iterations 0.1541030 4.566940 at 60iterations 7.7318750E-02 2.214392 at 70iterations 3.8518276E-02 1.107679 at 80iterations 1.9251095E-02 0.5910492 at 90iterations 9.6831582E-03 0.2829258 at 100iterations 4.9060588E-03 0.1477547 at 110iterations 2.5072587E-03 7.3665619E-02 at 120iterations finished qdiffx linear iterations at : 18:46:38 total time elapsed so far: 6.890000 # loops : 120 mean,max change (kT/e) : 2.5072587E-03 7.3665619E-02 energy calculations done at 6.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.070000 DelPhi exited at 18:46:38 7.068u 0.157s 0:07.72 93.3% 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 Mon Oct 10 2011 at 18:46:38 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2417 !!! WARNING: HIR 257 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: 3.150628 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): -14.58300 31.95400 ymin,ymax (A): -6.962000 40.17600 zmin,zma (A): 34.89500 85.74200 x,y,z range (A): 46.53700 47.13800 50.84701 scale (grids/A): 3.150628 object centre (A): 8.685501 16.60700 60.31850 number of atom coordinates read : 2417 total number of charged atoms : 2280 net assigned charge : 1.014006 assigned positive charge : 362.0128 centred at (gu) : 86.95848 97.45078 85.26347 assigned negative charge : -360.9995 centred at (gu) : 87.60535 97.46269 85.10006 start vw surface at 0.1100000 fill in re-entrant regions at 0.8100000 boundary points on vw surface= 204662 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21621 grid for indexing accessible points = 1.400000 m= 111186 mr = 149976 m= 46970 mr = 92259 m= 14177 mr = 38526 m= 2980 mr = 11050 m= 315 mr = 2142 m= 4 mr = 180 m= 0 mr = 0 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.900000 number of dielectric boundary points 86161 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.030000 number of grid points assigned charge 18236 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) : 2.100419 object centre at (A) : 8.685501 16.60700 60.31850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1812318 0.6335583 midg,1,midg; midg,igrid,midg -0.1188445 -8.3563522E-02 1,midg,midg; igrid,midg,midg 0.2260784 -0.1649607 gauss-seidel spectral radius is 0.9993165 estimated iterations to convergence 302 setup time was (sec) 2.180000 now iterating at: 18:46:41 rms-change max change #iterations 11.23590 357.3108 at 10iterations 6.737203 141.3568 at 20iterations 4.027557 85.24112 at 30iterations 2.400515 42.53896 at 40iterations 1.427024 26.54371 at 50iterations 0.8459062 15.25353 at 60iterations 0.4997355 8.679577 at 70iterations 0.2955779 5.026915 at 80iterations 0.1741598 3.363014 at 90iterations 0.1028252 1.674155 at 100iterations 6.0404893E-02 0.9999390 at 110iterations 3.5600834E-02 0.5770416 at 120iterations 2.0957559E-02 0.3444729 at 130iterations 1.2351790E-02 0.1921778 at 140iterations 7.2558164E-03 0.1354880 at 150iterations 4.2756950E-03 7.2188735E-02 at 160iterations 2.5162650E-03 3.9530754E-02 at 170iterations 1.4866312E-03 2.4553299E-02 at 180iterations finished qdiffx linear iterations at : 18:46:50 total time elapsed so far: 11.69000 # loops : 180 mean,max change (kT/e) : 1.4866312E-03 2.4553299E-02 energy calculations done at 11.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.85000 DelPhi exited at 18:46:51 11.857u 0.207s 0:12.59 95.7% 0+0k 0+0io 0pf+0w