Mon Oct 10 14:37:48 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 14:37:48 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2473 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: 0.6250439 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): -7.251000 44.23500 ymin,ymax (A): 12.95900 69.91500 zmin,zma (A): 55.19500 108.0550 x,y,z range (A): 51.48600 56.95600 52.86000 scale (grids/A): 0.6250439 object centre (A): 18.49200 41.43700 81.62500 number of atom coordinates read : 2473 total number of charged atoms : 2315 net assigned charge : -3.999990 assigned positive charge : 365.1081 centred at (gu) : 89.85345 90.78398 89.60144 assigned negative charge : -369.1084 centred at (gu) : 89.62769 90.74453 89.56734 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 6566 nv = 96 ne = 84 npr = 49580 no. pairs analyzed = 49580 no. exposed pairs = 3383 no. arc points = 23848 no. surface atoms = 1136 nbur = 1337 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 313 mr = 3331 m= 0 mr = 16 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3532 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2303 ## 222 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7805 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.7778996E-09 -1.1448640E-09 midg,1,midg; midg,igrid,midg -5.5849978E-09 -9.6670438E-10 1,midg,midg; igrid,midg,midg -2.1316726E-08 1.1970475E-08 gauss-seidel spectral radius is 0.9867388 estimated iterations to convergence 71 setup time was (sec) 0.5800000 now iterating at: 14:37:49 rms-change max change #iterations 0.1262950 27.32700 at 10iterations 1.1827177E-02 1.810246 at 20iterations 1.0822471E-03 0.1573324 at 30iterations 1.0311596E-04 1.8185616E-02 at 40iterations 9.5943542E-06 1.4514923E-03 at 50iterations finished qdiffx linear iterations at : 14:37:53 total time elapsed so far: 4.600000 # loops : 50 mean,max change (kT/e) : 9.5943542E-06 1.4514923E-03 energy calculations done at 4.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.770000 DelPhi exited at 14:37:53 4.776u 0.382s 0:05.45 94.4% 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 Mon Oct 10 2011 at 14:37:53 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2473 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: 1.875132 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): -7.251000 44.23500 ymin,ymax (A): 12.95900 69.91500 zmin,zma (A): 55.19500 108.0550 x,y,z range (A): 51.48600 56.95600 52.86000 scale (grids/A): 1.875132 object centre (A): 18.49200 41.43700 81.62500 number of atom coordinates read : 2473 total number of charged atoms : 2315 net assigned charge : -3.999990 assigned positive charge : 365.1081 centred at (gu) : 89.55970 92.35159 88.80374 assigned negative charge : -369.1084 centred at (gu) : 88.88269 92.23320 88.70176 start vw surface at 0.1200000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 70351 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23848 grid for indexing accessible points = 1.400000 m= 23634 mr = 46764 m= 3297 mr = 16405 m= 191 mr = 1659 m= 2 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 243 time to turn everything in is 0.5800000 number of dielectric boundary points 32619 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 176 iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 18181 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) : 0.6250439 object centre at (A) : 18.49200 41.43700 81.62500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1377170E-02 3.2433297E-03 midg,1,midg; midg,igrid,midg -3.1210121E-03 -1.4994870E-02 1,midg,midg; igrid,midg,midg -3.9524723E-02 4.9212524E-03 gauss-seidel spectral radius is 0.9985868 estimated iterations to convergence 211 setup time was (sec) 0.9400000 now iterating at: 14:37:54 rms-change max change #iterations 3.986273 172.8744 at 10iterations 1.830484 60.63477 at 20iterations 0.8451327 27.14082 at 30iterations 0.3906419 12.67248 at 40iterations 0.1795729 6.210962 at 50iterations 8.3061628E-02 2.641457 at 60iterations 3.8366936E-02 1.312522 at 70iterations 1.7690059E-02 0.5700095 at 80iterations 8.1578745E-03 0.2715282 at 90iterations 3.7590836E-03 0.1319222 at 100iterations 1.7378150E-03 6.1134338E-02 at 110iterations 8.0126117E-04 2.6138306E-02 at 120iterations finished qdiffx linear iterations at : 14:38:04 total time elapsed so far: 10.86000 # loops : 120 mean,max change (kT/e) : 8.0126117E-04 2.6138306E-02 energy calculations done at 10.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.03000 DelPhi exited at 14:38:05 11.037u 0.438s 0:11.96 95.8% 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 14:38:05 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: 292 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2473 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: 2.812697 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): -7.251000 44.23500 ymin,ymax (A): 12.95900 69.91500 zmin,zma (A): 55.19500 108.0550 x,y,z range (A): 51.48600 56.95600 52.86000 scale (grids/A): 2.812697 object centre (A): 18.49200 41.43700 81.62500 number of atom coordinates read : 2473 total number of charged atoms : 2315 net assigned charge : -3.999990 assigned positive charge : 365.1081 centred at (gu) : 89.33942 93.52729 88.20555 assigned negative charge : -369.1084 centred at (gu) : 88.32401 93.34966 88.05264 start vw surface at 0.1100000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 162858 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23848 grid for indexing accessible points = 1.400000 m= 77835 mr = 114261 m= 26089 mr = 61535 m= 5385 mr = 19715 m= 662 mr = 3434 m= 42 mr = 367 m= 0 mr = 7 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 893 time to turn everything in is 1.500000 number of dielectric boundary points 73552 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 18520 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) : 1.875132 object centre at (A) : 18.49200 41.43700 81.62500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3274971 2.4191217E-02 midg,1,midg; midg,igrid,midg -2.5118101E-02 -0.2137599 1,midg,midg; igrid,midg,midg -0.4183921 -1.7833985E-02 gauss-seidel spectral radius is 0.9992529 estimated iterations to convergence 289 setup time was (sec) 1.850000 now iterating at: 14:38:07 rms-change max change #iterations 9.624368 408.2276 at 10iterations 5.687584 147.5860 at 20iterations 3.325320 81.35170 at 30iterations 1.933560 42.79296 at 40iterations 1.120958 25.15128 at 50iterations 0.6481570 13.67227 at 60iterations 0.3746251 7.738741 at 70iterations 0.2157968 4.419642 at 80iterations 0.1241063 2.605074 at 90iterations 7.1416333E-02 1.356365 at 100iterations 4.1018341E-02 0.8298969 at 110iterations 2.3584966E-02 0.5237274 at 120iterations 1.3536297E-02 0.2512589 at 130iterations 7.7396519E-03 0.1653185 at 140iterations 4.4416217E-03 8.1635952E-02 at 150iterations 2.5457919E-03 4.6298981E-02 at 160iterations 1.4566219E-03 2.6345253E-02 at 170iterations 8.3498872E-04 1.5970290E-02 at 180iterations finished qdiffx linear iterations at : 14:38:24 total time elapsed so far: 18.11000 # loops : 180 mean,max change (kT/e) : 8.3498872E-04 1.5970290E-02 energy calculations done at 18.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.27000 DelPhi exited at 14:38:24 18.275u 0.461s 0:19.18 97.6% 0+0k 0+0io 0pf+0w