Sat Oct 8 22:07:04 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 Sat Oct 8 2011 at 22:07:04 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 = 2372 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: 0.6571054 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): -26.81900 26.03000 ymin,ymax (A): 7.867000 49.03300 zmin,zma (A): -12.78800 41.38900 x,y,z range (A): 52.84900 41.16600 54.17700 scale (grids/A): 0.6571054 object centre (A): -0.3945007 28.45000 14.30050 number of atom coordinates read : 2372 total number of charged atoms : 2237 net assigned charge : 11.00002 assigned positive charge : 344.6333 centred at (gu) : 90.39363 90.95638 91.37247 assigned negative charge : -333.6341 centred at (gu) : 90.40857 90.89925 91.34810 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6889 nv = 96 ne = 84 npr = 48351 no. pairs analyzed = 48351 no. exposed pairs = 3119 no. arc points = 22118 no. surface atoms = 1046 nbur = 1326 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 390 mr = 3585 m= 0 mr = 46 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1800000 number of dielectric boundary points 3648 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2163 ## 180 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 8233 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.6609020E-08 3.9007748E-08 midg,1,midg; midg,igrid,midg 1.3775145E-08 4.2086057E-08 1,midg,midg; igrid,midg,midg 2.5843198E-08 2.5187884E-08 gauss-seidel spectral radius is 0.9879810 estimated iterations to convergence 74 setup time was (sec) 0.3800000 now iterating at: 22:07:04 rms-change max change #iterations 0.1443053 22.46791 at 10iterations 1.5455437E-02 2.221277 at 20iterations 1.6343154E-03 0.2505417 at 30iterations 1.9848044E-04 2.6397705E-02 at 40iterations 3.6086072E-05 5.0888062E-03 at 50iterations finished qdiffx linear iterations at : 22:07:07 total time elapsed so far: 3.420000 # loops : 50 mean,max change (kT/e) : 3.6086072E-05 5.0888062E-03 energy calculations done at 3.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.560000 DelPhi exited at 22:07:08 3.568u 0.189s 0:04.04 92.5% 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 Sat Oct 8 2011 at 22:07:08 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 = 2372 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: 1.971316 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): -26.81900 26.03000 ymin,ymax (A): 7.867000 49.03300 zmin,zma (A): -12.78800 41.38900 x,y,z range (A): 52.84900 41.16600 54.17700 scale (grids/A): 1.971316 object centre (A): -0.3945007 28.45000 14.30050 number of atom coordinates read : 2372 total number of charged atoms : 2237 net assigned charge : 11.00002 assigned positive charge : 344.6333 centred at (gu) : 91.18060 92.86877 94.11703 assigned negative charge : -333.6341 centred at (gu) : 91.22560 92.69775 94.04424 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 73770 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22118 grid for indexing accessible points = 1.400000 m= 26099 mr = 49554 m= 4369 mr = 18667 m= 297 mr = 2801 m= 5 mr = 124 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 362 time to turn everything in is 0.3800000 number of dielectric boundary points 33394 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 140 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 17680 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) : 0.6571054 object centre at (A) : -0.3945007 28.45000 14.30050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0989958E-02 2.6277516E-02 midg,1,midg; midg,igrid,midg 4.0465132E-03 3.2334447E-02 1,midg,midg; igrid,midg,midg 5.7525069E-02 5.5830680E-02 gauss-seidel spectral radius is 0.9987049 estimated iterations to convergence 220 setup time was (sec) 0.6100000 now iterating at: 22:07:09 rms-change max change #iterations 4.181157 191.4944 at 10iterations 1.992895 71.50520 at 20iterations 0.9478522 31.50812 at 30iterations 0.4540042 15.24720 at 40iterations 0.2164710 6.628157 at 50iterations 0.1030532 3.441653 at 60iterations 4.9125742E-02 1.573537 at 70iterations 2.3493996E-02 0.6881905 at 80iterations 1.1267480E-02 0.3769665 at 90iterations 5.3567039E-03 0.1696053 at 100iterations 2.5672694E-03 7.7116013E-02 at 110iterations 1.2227645E-03 3.6720276E-02 at 120iterations finished qdiffx linear iterations at : 22:07:16 total time elapsed so far: 8.160000 # loops : 120 mean,max change (kT/e) : 1.2227645E-03 3.6720276E-02 energy calculations done at 8.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.290000 DelPhi exited at 22:07:17 8.294u 0.229s 0:08.82 96.4% 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 22:07:17 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 = 2372 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: 2.956975 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): -26.81900 26.03000 ymin,ymax (A): 7.867000 49.03300 zmin,zma (A): -12.78800 41.38900 x,y,z range (A): 52.84900 41.16600 54.17700 scale (grids/A): 2.956975 object centre (A): -0.3945007 28.45000 14.30050 number of atom coordinates read : 2372 total number of charged atoms : 2237 net assigned charge : 11.00002 assigned positive charge : 344.6333 centred at (gu) : 91.77081 94.30293 96.17556 assigned negative charge : -333.6341 centred at (gu) : 91.83842 94.04665 96.06640 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 170681 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22118 grid for indexing accessible points = 1.400000 m= 83853 mr = 120932 m= 30745 mr = 67054 m= 7962 mr = 24365 m= 1330 mr = 6004 m= 96 mr = 929 m= 2 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.5600001 no. cavity mid-points inaccessible to solvent = 1212 time to turn everything in is 1.000000 number of dielectric boundary points 75346 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 17896 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) : 1.971316 object centre at (A) : -0.3945007 28.45000 14.30050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5044933 0.2713076 midg,1,midg; midg,igrid,midg 1.3649589E-02 0.3200080 1,midg,midg; igrid,midg,midg 0.6542410 0.5479675 gauss-seidel spectral radius is 0.9992830 estimated iterations to convergence 295 setup time was (sec) 1.310000 now iterating at: 22:07:18 rms-change max change #iterations 9.783801 413.2832 at 10iterations 5.782602 125.4774 at 20iterations 3.398276 80.50465 at 30iterations 1.994606 45.59322 at 40iterations 1.167965 23.08279 at 50iterations 0.6842052 15.48608 at 60iterations 0.3987562 7.378898 at 70iterations 0.2327586 4.183359 at 80iterations 0.1357639 2.521323 at 90iterations 7.9011239E-02 1.528202 at 100iterations 4.5915794E-02 0.8399973 at 110iterations 2.6757047E-02 0.5077209 at 120iterations 1.5557173E-02 0.3317184 at 130iterations 9.0485578E-03 0.1634064 at 140iterations 5.2663083E-03 0.1026154 at 150iterations 3.0630494E-03 5.7680607E-02 at 160iterations 1.7843095E-03 3.2749176E-02 at 170iterations 1.0481707E-03 2.2996902E-02 at 180iterations finished qdiffx linear iterations at : 22:07:32 total time elapsed so far: 15.06000 # loops : 180 mean,max change (kT/e) : 1.0481707E-03 2.2996902E-02 energy calculations done at 15.06000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.19000 DelPhi exited at 22:07:33 15.192u 0.309s 0:15.75 98.3% 0+0k 0+0io 0pf+0w