Mon Oct 10 14:01:43 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 14:01:43 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2420 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: 0.6876968 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): -14.05400 37.71300 ymin,ymax (A): 0.6020001 44.45100 zmin,zma (A): -7.365000 44.09000 x,y,z range (A): 51.76700 43.84900 51.45500 scale (grids/A): 0.6876968 object centre (A): 11.82950 22.52650 18.36250 number of atom coordinates read : 2420 total number of charged atoms : 2278 net assigned charge : 3.500024 assigned positive charge : 373.4411 centred at (gu) : 90.83184 91.18528 90.03036 assigned negative charge : -369.9416 centred at (gu) : 91.02146 91.24995 89.99316 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 7622 nv = 96 ne = 84 npr = 48787 no. pairs analyzed = 48787 no. exposed pairs = 3048 no. arc points = 21122 no. surface atoms = 1017 nbur = 1403 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 465 mr = 4209 m= 0 mr = 71 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3807 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1966 ## 188 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8746 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.3941340E-09 3.3279225E-08 midg,1,midg; midg,igrid,midg 3.4141873E-08 -6.5938703E-09 1,midg,midg; igrid,midg,midg 7.4828677E-08 -6.2646748E-08 gauss-seidel spectral radius is 0.9890167 estimated iterations to convergence 78 setup time was (sec) 0.3800000 now iterating at: 14:01:44 rms-change max change #iterations 0.1985222 26.90895 at 10iterations 2.3409966E-02 3.120386 at 20iterations 3.2152922E-03 0.4345016 at 30iterations 7.1108976E-04 0.1135788 at 40iterations 2.3314184E-04 3.8017273E-02 at 50iterations finished qdiffx linear iterations at : 14:01:46 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 2.3314184E-04 3.8017273E-02 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 14:01:47 3.335u 0.149s 0:04.47 77.6% 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 14:01:48 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2420 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: 2.063091 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): -14.05400 37.71300 ymin,ymax (A): 0.6020001 44.45100 zmin,zma (A): -7.365000 44.09000 x,y,z range (A): 51.76700 43.84900 51.45500 scale (grids/A): 2.063091 object centre (A): 11.82950 22.52650 18.36250 number of atom coordinates read : 2420 total number of charged atoms : 2278 net assigned charge : 3.500024 assigned positive charge : 373.4411 centred at (gu) : 92.49519 93.55540 90.09081 assigned negative charge : -369.9416 centred at (gu) : 93.06431 93.74955 89.97923 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 80361 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21122 grid for indexing accessible points = 1.400000 m= 30920 mr = 55614 m= 5774 mr = 23034 m= 557 mr = 3789 m= 9 mr = 309 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 34875 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 112 iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 18072 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) : 0.6876968 object centre at (A) : 11.82950 22.52650 18.36250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.4147557E-02 2.2263287E-02 midg,1,midg; midg,igrid,midg 3.6388226E-02 3.4133969E-03 1,midg,midg; igrid,midg,midg 1.8680358E-02 -6.3428380E-02 gauss-seidel spectral radius is 0.9988096 estimated iterations to convergence 229 setup time was (sec) 0.6100000 now iterating at: 14:01:48 rms-change max change #iterations 4.915695 198.6910 at 10iterations 2.412446 73.17220 at 20iterations 1.189341 34.67555 at 30iterations 0.5865422 18.64067 at 40iterations 0.2897370 8.290573 at 50iterations 0.1429577 4.340394 at 60iterations 7.0355900E-02 1.903419 at 70iterations 3.4877028E-02 1.087242 at 80iterations 1.7302755E-02 0.5457175 at 90iterations 8.6469986E-03 0.2602305 at 100iterations 4.4051507E-03 0.1325922 at 110iterations 2.3120467E-03 7.5531006E-02 at 120iterations finished qdiffx linear iterations at : 14:01:55 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 2.3120467E-03 7.5531006E-02 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 14:01:56 7.719u 0.198s 0:08.59 91.9% 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 14:01:56 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2420 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: 3.094636 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): -14.05400 37.71300 ymin,ymax (A): 0.6020001 44.45100 zmin,zma (A): -7.365000 44.09000 x,y,z range (A): 51.76700 43.84900 51.45500 scale (grids/A): 3.094636 object centre (A): 11.82950 22.52650 18.36250 number of atom coordinates read : 2420 total number of charged atoms : 2278 net assigned charge : 3.500024 assigned positive charge : 373.4411 centred at (gu) : 93.74251 95.33295 90.13613 assigned negative charge : -369.9416 centred at (gu) : 94.59632 95.62433 89.96877 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 185344 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21122 grid for indexing accessible points = 1.400000 m= 96989 mr = 134382 m= 38477 mr = 79493 m= 10775 mr = 31273 m= 2155 mr = 8280 m= 280 mr = 1680 m= 4 mr = 183 m= 0 mr = 0 time to grow re-entrant surface = 0.6200001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.230000 number of dielectric boundary points 78733 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.330000 number of grid points assigned charge 18224 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) : 2.063091 object centre at (A) : 11.82950 22.52650 18.36250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3670332 0.1026888 midg,1,midg; midg,igrid,midg 0.3279213 -6.2160760E-02 1,midg,midg; igrid,midg,midg 0.3322158 -0.6693405 gauss-seidel spectral radius is 0.9992957 estimated iterations to convergence 297 setup time was (sec) 1.480000 now iterating at: 14:01:58 rms-change max change #iterations 11.05063 458.1814 at 10iterations 6.549084 156.5650 at 20iterations 3.876481 80.41183 at 30iterations 2.281551 43.96750 at 40iterations 1.341759 29.99776 at 50iterations 0.7904487 17.99135 at 60iterations 0.4620097 8.696453 at 70iterations 0.2706909 4.578430 at 80iterations 0.1584620 3.070492 at 90iterations 9.2963949E-02 1.540619 at 100iterations 5.4540023E-02 0.9342575 at 110iterations 3.2139264E-02 0.5456009 at 120iterations 1.9116111E-02 0.3296585 at 130iterations 1.1484777E-02 0.1975965 at 140iterations 7.0963660E-03 0.1364555 at 150iterations 4.5887991E-03 9.5069885E-02 at 160iterations 3.1328239E-03 6.7874908E-02 at 170iterations 2.2832947E-03 5.1246643E-02 at 180iterations finished qdiffx linear iterations at : 14:02:09 total time elapsed so far: 12.65000 # loops : 180 mean,max change (kT/e) : 2.2832947E-03 5.1246643E-02 energy calculations done at 12.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.77000 DelPhi exited at 14:02:10 12.773u 0.181s 0:13.84 93.5% 0+0k 0+0io 0pf+0w