Wed Nov 16 01:35:54 PST 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 Wed Nov 16 2011 at 01:35:54 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 ! Automatically converted by prot2crg.py # of charge parameter records: 922 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1965 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: 0.5681636 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): -26.84300 35.81500 ymin,ymax (A): -18.95400 20.71900 zmin,zma (A): -3.147000 38.71200 x,y,z range (A): 62.65800 39.67300 41.85900 scale (grids/A): 0.5681636 object centre (A): 4.486001 0.8824997 17.78250 number of atom coordinates read : 1965 total number of charged atoms : 1833 net assigned charge : 3.000004 assigned positive charge : 290.5330 centred at (gu) : 90.27944 90.17612 90.44766 assigned negative charge : -287.5333 centred at (gu) : 90.29182 90.27274 90.58609 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 4215 nv = 96 ne = 84 npr = 40270 no. pairs analyzed = 40270 no. exposed pairs = 2416 no. arc points = 16960 no. surface atoms = 818 nbur = 1147 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 143 mr = 2287 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 2069 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1784 ## 251 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 5299 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5635416E-09 -1.0090968E-09 midg,1,midg; midg,igrid,midg 1.2967778E-09 -5.1433180E-10 1,midg,midg; igrid,midg,midg 5.2374799E-10 3.4408021E-10 gauss-seidel spectral radius is 0.9839328 estimated iterations to convergence 65 setup time was (sec) 0.3900000 now iterating at: 01:35:55 rms-change max change #iterations 7.1002148E-02 12.85767 at 10iterations 5.3474908E-03 0.9494696 at 20iterations 3.8985963E-04 6.7528725E-02 at 30iterations 2.8183249E-05 4.8675537E-03 at 40iterations 2.1594133E-06 4.3296814E-04 at 50iterations finished qdiffx linear iterations at : 01:35:58 total time elapsed so far: 3.340000 # loops : 50 mean,max change (kT/e) : 2.1594133E-06 4.3296814E-04 energy calculations done at 3.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 01:35:58 3.491u 0.181s 0:04.15 88.4% 0+0k 0+45552io 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 Wed Nov 16 2011 at 01:35:58 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 ! Automatically converted by prot2crg.py # of charge parameter records: 922 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1965 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: 1.704491 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): -26.84300 35.81500 ymin,ymax (A): -18.95400 20.71900 zmin,zma (A): -3.147000 38.71200 x,y,z range (A): 62.65800 39.67300 41.85900 scale (grids/A): 1.704491 object centre (A): 4.486001 0.8824997 17.78250 number of atom coordinates read : 1965 total number of charged atoms : 1833 net assigned charge : 3.000004 assigned positive charge : 290.5330 centred at (gu) : 90.83842 90.52811 91.34303 assigned negative charge : -287.5333 centred at (gu) : 90.87566 90.81841 91.75845 start vw surface at 0.1000000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 46578 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16960 grid for indexing accessible points = 1.400000 m= 15479 mr = 31884 m= 1579 mr = 11659 m= 32 mr = 865 m= 0 mr = 5 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 652 time to turn everything in is 0.3000000 number of dielectric boundary points 19255 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 211 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 14188 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) : 0.5681636 object centre at (A) : 4.486001 0.8824997 17.78250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9437249E-03 -6.5891999E-03 midg,1,midg; midg,igrid,midg 2.7163664E-03 -2.0021521E-03 1,midg,midg; igrid,midg,midg 2.7495237E-02 2.7486093E-02 gauss-seidel spectral radius is 0.9982152 estimated iterations to convergence 188 setup time was (sec) 0.5000000 now iterating at: 01:35:59 rms-change max change #iterations 2.842194 150.6624 at 10iterations 1.191869 62.12851 at 20iterations 0.4997814 21.55616 at 30iterations 0.2098559 9.096339 at 40iterations 8.8351868E-02 3.654753 at 50iterations 3.7060872E-02 1.708168 at 60iterations 1.5626321E-02 0.6715765 at 70iterations 6.5601151E-03 0.2620692 at 80iterations 2.7541139E-03 0.1050844 at 90iterations 1.1601017E-03 4.6421051E-02 at 100iterations 4.8659745E-04 1.9872665E-02 at 110iterations 2.0366292E-04 8.4698200E-03 at 120iterations finished qdiffx linear iterations at : 01:36:06 total time elapsed so far: 7.570000 # loops : 120 mean,max change (kT/e) : 2.0366292E-04 8.4698200E-03 energy calculations done at 7.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.710000 DelPhi exited at 01:36:06 7.720u 0.200s 0:08.20 96.5% 0+0k 0+45144io 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 Wed Nov 16 2011 at 01:36:06 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 ! Automatically converted by prot2crg.py # of charge parameter records: 922 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1965 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: 2.556736 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): -26.84300 35.81500 ymin,ymax (A): -18.95400 20.71900 zmin,zma (A): -3.147000 38.71200 x,y,z range (A): 62.65800 39.67300 41.85900 scale (grids/A): 2.556736 object centre (A): 4.486001 0.8824997 17.78250 number of atom coordinates read : 1965 total number of charged atoms : 1833 net assigned charge : 3.000004 assigned positive charge : 290.5330 centred at (gu) : 91.25757 90.79230 92.01449 assigned negative charge : -287.5333 centred at (gu) : 91.31349 91.22772 92.63778 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 107819 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16960 grid for indexing accessible points = 1.400000 m= 52904 mr = 77506 m= 16070 mr = 43550 m= 2479 mr = 13033 m= 147 mr = 1738 m= 1 mr = 62 m= 0 mr = 0 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 2169 time to turn everything in is 0.7200000 number of dielectric boundary points 43531 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 14658 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) : 1.704491 object centre at (A) : 4.486001 0.8824997 17.78250 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.7130394E-02 -7.3687747E-02 midg,1,midg; midg,igrid,midg 2.5870191E-02 -2.1427033E-02 1,midg,midg; igrid,midg,midg 0.3627020 0.3642571 gauss-seidel spectral radius is 0.9991130 estimated iterations to convergence 265 setup time was (sec) 0.9300000 now iterating at: 01:36:08 rms-change max change #iterations 7.088268 264.5671 at 10iterations 3.887451 124.8736 at 20iterations 2.121646 60.15679 at 30iterations 1.158402 29.03232 at 40iterations 0.6301199 14.72977 at 50iterations 0.3423354 8.739206 at 60iterations 0.1861299 4.122493 at 70iterations 0.1010429 2.418178 at 80iterations 5.4983649E-02 1.300189 at 90iterations 2.9949088E-02 0.6951523 at 100iterations 1.6217319E-02 0.3687096 at 110iterations 8.8575818E-03 0.2062778 at 120iterations 4.8065470E-03 0.1073217 at 130iterations 2.6089209E-03 6.9035053E-02 at 140iterations 1.4186436E-03 3.1515121E-02 at 150iterations 7.7163690E-04 1.9100189E-02 at 160iterations 4.2029750E-04 9.5648766E-03 at 170iterations 2.2781154E-04 5.2890778E-03 at 180iterations finished qdiffx linear iterations at : 01:36:18 total time elapsed so far: 11.84000 # loops : 180 mean,max change (kT/e) : 2.2781154E-04 5.2890778E-03 energy calculations done at 11.84000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.98000 DelPhi exited at 01:36:19 11.988u 0.221s 0:12.52 97.4% 0+0k 0+45136io 0pf+0w