Sun Oct 9 16:07:59 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 Sun Oct 9 2011 at 16:07:59 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 = 3120 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: 0.6324392 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): -15.20700 36.89800 ymin,ymax (A): 55.67600 107.8860 zmin,zma (A): -3.868000 52.42200 x,y,z range (A): 52.10500 52.21000 56.29000 scale (grids/A): 0.6324392 object centre (A): 10.84550 81.78101 24.27700 number of atom coordinates read : 3120 total number of charged atoms : 2975 net assigned charge : -4.499987 assigned positive charge : 462.7409 centred at (gu) : 90.09656 88.53082 91.19222 assigned negative charge : -467.2423 centred at (gu) : 90.14412 88.39320 91.26923 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 8227 nv = 96 ne = 84 npr = 64836 no. pairs analyzed = 64836 no. exposed pairs = 3889 no. arc points = 26731 no. surface atoms = 1324 nbur = 1796 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 500 mr = 4478 m= 2 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 4178 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2623 ## 218 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 10089 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8897149E-09 -1.7708290E-08 midg,1,midg; midg,igrid,midg -2.8594942E-08 7.5839370E-09 1,midg,midg; igrid,midg,midg 5.0996207E-10 -1.0485551E-08 gauss-seidel spectral radius is 0.9870933 estimated iterations to convergence 72 setup time was (sec) 0.6000000 now iterating at: 16:08:00 rms-change max change #iterations 0.1546211 22.64520 at 10iterations 1.4800336E-02 2.113363 at 20iterations 1.4296572E-03 0.1921377 at 30iterations 1.3823590E-04 1.7785788E-02 at 40iterations 1.4128233E-05 1.9912720E-03 at 50iterations finished qdiffx linear iterations at : 16:08:02 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 1.4128233E-05 1.9912720E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 16:08:03 3.453u 0.159s 0:03.89 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 Sun Oct 9 2011 at 16:08:03 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 = 3120 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: 1.897318 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): -15.20700 36.89800 ymin,ymax (A): 55.67600 107.8860 zmin,zma (A): -3.868000 52.42200 x,y,z range (A): 52.10500 52.21000 56.29000 scale (grids/A): 1.897318 object centre (A): 10.84550 81.78101 24.27700 number of atom coordinates read : 3120 total number of charged atoms : 2975 net assigned charge : -4.499987 assigned positive charge : 462.7409 centred at (gu) : 90.28883 85.59166 93.57587 assigned negative charge : -467.2423 centred at (gu) : 90.43238 85.17943 93.80750 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 89086 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26731 grid for indexing accessible points = 1.400000 m= 32143 mr = 62005 m= 5430 mr = 23097 m= 313 mr = 3318 m= 6 mr = 97 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 193 time to turn everything in is 0.6600000 number of dielectric boundary points 38461 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 159 iepsmp to db, and charging done at 0.7900000 number of grid points assigned charge 23433 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) : 0.6324392 object centre at (A) : 10.84550 81.78101 24.27700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3494115E-02 1.0769684E-02 midg,1,midg; midg,igrid,midg -3.5117775E-02 -9.4370721E-03 1,midg,midg; igrid,midg,midg -3.5150919E-02 -3.3735298E-02 gauss-seidel spectral radius is 0.9986684 estimated iterations to convergence 217 setup time was (sec) 0.9500000 now iterating at: 16:08:04 rms-change max change #iterations 4.642928 206.2347 at 10iterations 2.191051 80.67677 at 20iterations 1.034786 31.90411 at 30iterations 0.4878102 13.76192 at 40iterations 0.2314340 7.346531 at 50iterations 0.1094387 3.180511 at 60iterations 5.1735960E-02 1.588089 at 70iterations 2.4445623E-02 0.7010193 at 80iterations 1.1538814E-02 0.3403425 at 90iterations 5.4564802E-03 0.1629562 at 100iterations 2.5832201E-03 8.6085320E-02 at 110iterations 1.2242788E-03 3.6496103E-02 at 120iterations finished qdiffx linear iterations at : 16:08:10 total time elapsed so far: 7.480000 # loops : 120 mean,max change (kT/e) : 1.2242788E-03 3.6496103E-02 energy calculations done at 7.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.670000 DelPhi exited at 16:08:11 7.670u 0.170s 0:08.12 96.5% 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 Sun Oct 9 2011 at 16:08:11 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 = 3120 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: 2.845976 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): -15.20700 36.89800 ymin,ymax (A): 55.67600 107.8860 zmin,zma (A): -3.868000 52.42200 x,y,z range (A): 52.10500 52.21000 56.29000 scale (grids/A): 2.845976 object centre (A): 10.84550 81.78101 24.27700 number of atom coordinates read : 3120 total number of charged atoms : 2975 net assigned charge : -4.499987 assigned positive charge : 462.7409 centred at (gu) : 90.43286 83.38739 95.36363 assigned negative charge : -467.2423 centred at (gu) : 90.64853 82.76914 95.71110 start vw surface at 0.1600000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 206507 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26731 grid for indexing accessible points = 1.400000 m= 103262 mr = 151149 m= 38597 mr = 83285 m= 9935 mr = 30319 m= 1331 mr = 7332 m= 67 mr = 836 m= 0 mr = 32 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 638 time to turn everything in is 1.690000 number of dielectric boundary points 86746 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.830000 number of grid points assigned charge 23797 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) : 1.897318 object centre at (A) : 10.84550 81.78101 24.27700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4715107 0.2732160 midg,1,midg; midg,igrid,midg -0.3724516 -0.2277263 1,midg,midg; igrid,midg,midg -0.5067903 -0.3430525 gauss-seidel spectral radius is 0.9992798 estimated iterations to convergence 294 setup time was (sec) 1.990000 now iterating at: 16:08:13 rms-change max change #iterations 10.89593 327.0646 at 10iterations 6.419831 146.5950 at 20iterations 3.757342 70.39396 at 30iterations 2.194601 45.11179 at 40iterations 1.282439 23.15919 at 50iterations 0.7469682 13.28280 at 60iterations 0.4347019 7.798561 at 70iterations 0.2530404 4.783795 at 80iterations 0.1471034 2.467979 at 90iterations 8.5479133E-02 1.599073 at 100iterations 4.9633976E-02 1.028296 at 110iterations 2.8795669E-02 0.5331841 at 120iterations 1.6676325E-02 0.2840958 at 130iterations 9.6720336E-03 0.1655874 at 140iterations 5.6293998E-03 9.8243952E-02 at 150iterations 3.2551098E-03 5.6214213E-02 at 160iterations 1.8911219E-03 3.2119751E-02 at 170iterations 1.1003676E-03 1.9598007E-02 at 180iterations finished qdiffx linear iterations at : 16:08:24 total time elapsed so far: 12.54000 # loops : 180 mean,max change (kT/e) : 1.1003676E-03 1.9598007E-02 energy calculations done at 12.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.72000 DelPhi exited at 16:08:24 12.722u 0.194s 0:13.19 97.8% 0+0k 0+0io 0pf+0w