Tue Oct 11 06:00:44 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 06:00:44 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.7041557 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): 25.57000 72.41200 ymin,ymax (A): -18.93400 31.62300 zmin,zma (A): 3.881000 46.31400 x,y,z range (A): 46.84200 50.55700 42.43300 scale (grids/A): 0.7041557 object centre (A): 48.99100 6.344501 25.09750 number of atom coordinates read : 2327 total number of charged atoms : 2002 net assigned charge : 6.500009 assigned positive charge : 325.3439 centred at (gu) : 89.21127 90.22217 90.36843 assigned negative charge : -318.8441 centred at (gu) : 89.32867 90.17513 90.45629 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 7167 nv = 96 ne = 84 npr = 42269 no. pairs analyzed = 42269 no. exposed pairs = 2616 no. arc points = 17848 no. surface atoms = 904 nbur = 1423 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 482 mr = 4107 m= 3 mr = 86 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3459 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1642 ## 151 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8040 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.4989203E-08 9.2173371E-09 midg,1,midg; midg,igrid,midg 2.7108117E-08 7.5525548E-08 1,midg,midg; igrid,midg,midg 1.2235654E-07 -4.1774224E-09 gauss-seidel spectral radius is 0.9894920 estimated iterations to convergence 79 setup time was (sec) 0.5600000 now iterating at: 06:00:45 rms-change max change #iterations 0.1968456 26.30363 at 10iterations 2.4422802E-02 3.078140 at 20iterations 3.2926728E-03 0.4443855 at 30iterations 6.1358302E-04 7.9620361E-02 at 40iterations 1.7376071E-04 2.0194054E-02 at 50iterations finished qdiffx linear iterations at : 06:00:49 total time elapsed so far: 4.230000 # loops : 50 mean,max change (kT/e) : 1.7376071E-04 2.0194054E-02 energy calculations done at 4.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.410000 DelPhi exited at 06:00:49 4.411u 0.413s 0:05.12 94.1% 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 Tue Oct 11 2011 at 06:00:49 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 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: 2.112467 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): 25.57000 72.41200 ymin,ymax (A): -18.93400 31.62300 zmin,zma (A): 3.881000 46.31400 x,y,z range (A): 46.84200 50.55700 42.43300 scale (grids/A): 2.112467 object centre (A): 48.99100 6.344501 25.09750 number of atom coordinates read : 2327 total number of charged atoms : 2002 net assigned charge : 6.500009 assigned positive charge : 325.3439 centred at (gu) : 87.63364 90.66639 91.10520 assigned negative charge : -318.8441 centred at (gu) : 87.98586 90.52549 91.36874 start vw surface at 0.1200000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 76120 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17848 grid for indexing accessible points = 1.400000 m= 31195 mr = 54239 m= 5934 mr = 23855 m= 541 mr = 3914 m= 21 mr = 244 m= 0 mr = 2 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6600000 number of dielectric boundary points 31557 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 62 iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 15879 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) : 0.7041557 object centre at (A) : 48.99100 6.344501 25.09750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.4938971E-02 2.5499733E-02 midg,1,midg; midg,igrid,midg 4.5325872E-02 2.3928259E-02 1,midg,midg; igrid,midg,midg 4.2961169E-02 -4.0036201E-02 gauss-seidel spectral radius is 0.9988266 estimated iterations to convergence 231 setup time was (sec) 1.000000 now iterating at: 06:00:51 rms-change max change #iterations 4.632273 178.6818 at 10iterations 2.282240 85.14053 at 20iterations 1.130953 34.22215 at 30iterations 0.5609143 16.96489 at 40iterations 0.2783236 8.395319 at 50iterations 0.1381937 4.117035 at 60iterations 6.8422623E-02 1.963782 at 70iterations 3.4015957E-02 1.039352 at 80iterations 1.7003002E-02 0.5565014 at 90iterations 8.4795430E-03 0.2658863 at 100iterations 4.2800405E-03 0.1279678 at 110iterations 2.2025809E-03 6.4862251E-02 at 120iterations finished qdiffx linear iterations at : 06:01:00 total time elapsed so far: 10.44000 # loops : 120 mean,max change (kT/e) : 2.2025809E-03 6.4862251E-02 energy calculations done at 10.44000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.59000 DelPhi exited at 06:01:01 10.599u 0.462s 0:11.56 95.5% 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 06:01:01 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: 255 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2327 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 3.168701 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): 25.57000 72.41200 ymin,ymax (A): -18.93400 31.62300 zmin,zma (A): 3.881000 46.31400 x,y,z range (A): 46.84200 50.55700 42.43300 scale (grids/A): 3.168701 object centre (A): 48.99100 6.344501 25.09750 number of atom coordinates read : 2327 total number of charged atoms : 2002 net assigned charge : 6.500009 assigned positive charge : 325.3439 centred at (gu) : 86.45043 90.99969 91.65775 assigned negative charge : -318.8441 centred at (gu) : 86.97878 90.78828 92.05313 start vw surface at 0.1200000 fill in re-entrant regions at 0.7900000 boundary points on vw surface= 175191 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17848 grid for indexing accessible points = 1.400000 m= 96598 mr = 130173 m= 39738 mr = 80822 m= 11241 mr = 32775 m= 2169 mr = 8649 m= 263 mr = 1545 m= 12 mr = 167 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 1.090000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.010000 number of dielectric boundary points 71081 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.120000 number of grid points assigned charge 16016 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) : 2.112467 object centre at (A) : 48.99100 6.344501 25.09750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1619935 0.2142291 midg,1,midg; midg,igrid,midg 0.3739144 9.3339704E-02 1,midg,midg; igrid,midg,midg 0.4241879 -0.4980373 gauss-seidel spectral radius is 0.9992972 estimated iterations to convergence 298 setup time was (sec) 2.320000 now iterating at: 06:01:04 rms-change max change #iterations 10.38030 436.8412 at 10iterations 6.156022 128.1546 at 20iterations 3.645073 79.32933 at 30iterations 2.149102 38.60032 at 40iterations 1.268442 25.29383 at 50iterations 0.7471851 15.91736 at 60iterations 0.4387594 8.081359 at 70iterations 0.2567594 4.749957 at 80iterations 0.1509664 2.759926 at 90iterations 8.8437706E-02 1.780141 at 100iterations 5.1950779E-02 0.9893510 at 110iterations 3.0458501E-02 0.5682526 at 120iterations 1.7988224E-02 0.3311863 at 130iterations 1.0726594E-02 0.1946392 at 140iterations 6.4675850E-03 0.1129475 at 150iterations 3.9921124E-03 8.4030151E-02 at 160iterations 2.5712468E-03 4.8643112E-02 at 170iterations 1.7495528E-03 3.1887054E-02 at 180iterations finished qdiffx linear iterations at : 06:01:20 total time elapsed so far: 18.12000 # loops : 180 mean,max change (kT/e) : 1.7495528E-03 3.1887054E-02 energy calculations done at 18.12000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.28000 DelPhi exited at 06:01:20 18.281u 0.491s 0:19.28 97.3% 0+0k 0+0io 0pf+0w