Sat Oct 8 12:56:26 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 Sat Oct 8 2011 at 12:56:26 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1282 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7151179 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): -0.8800000 42.44700 ymin,ymax (A): -18.52500 20.30300 zmin,zma (A): -14.05800 35.72400 x,y,z range (A): 43.32700 38.82800 49.78200 scale (grids/A): 0.7151179 object centre (A): 20.78350 0.8889999 10.83300 number of atom coordinates read : 1282 total number of charged atoms : 1147 net assigned charge : 2.000010 assigned positive charge : 189.4882 centred at (gu) : 89.82240 89.42873 90.21537 assigned negative charge : -187.4880 centred at (gu) : 89.85619 89.20974 89.75652 start vw surface at 0.1300000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 4560 nv = 96 ne = 84 npr = 25344 no. pairs analyzed = 25344 no. exposed pairs = 1740 no. arc points = 13222 no. surface atoms = 586 nbur = 696 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 280 mr = 2217 m= 5 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 8.0000013E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 2582 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1094 ## 114 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 4682 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4202901E-07 1.8274321E-07 midg,1,midg; midg,igrid,midg -6.5113902E-08 8.6097721E-08 1,midg,midg; igrid,midg,midg 3.3769105E-08 8.5894420E-09 gauss-seidel spectral radius is 0.9897370 estimated iterations to convergence 80 setup time was (sec) 0.5000000 now iterating at: 12:56:27 rms-change max change #iterations 0.1630950 30.10466 at 10iterations 1.9814791E-02 3.705452 at 20iterations 2.4614951E-03 0.4685135 at 30iterations 3.0628731E-04 5.1353455E-02 at 40iterations 3.7478778E-05 6.3152313E-03 at 50iterations finished qdiffx linear iterations at : 12:56:30 total time elapsed so far: 3.830000 # loops : 50 mean,max change (kT/e) : 3.7478778E-05 6.3152313E-03 energy calculations done at 3.830000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.020000 DelPhi exited at 12:56:31 4.024u 0.262s 0:04.55 94.0% 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 Sat Oct 8 2011 at 12:56:31 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1282 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.145354 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): -0.8800000 42.44700 ymin,ymax (A): -18.52500 20.30300 zmin,zma (A): -14.05800 35.72400 x,y,z range (A): 43.32700 38.82800 49.78200 scale (grids/A): 2.145354 object centre (A): 20.78350 0.8889999 10.83300 number of atom coordinates read : 1282 total number of charged atoms : 1147 net assigned charge : 2.000010 assigned positive charge : 189.4882 centred at (gu) : 89.46726 88.28634 90.64626 assigned negative charge : -187.4880 centred at (gu) : 89.56871 87.62922 89.26959 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 46940 reading accessible surface arcs data from file ARCDAT no. of arc points read = 13222 grid for indexing accessible points = 1.400000 m= 16967 mr = 29766 m= 3630 mr = 12047 m= 417 mr = 2264 m= 10 mr = 178 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4700000 number of dielectric boundary points 23709 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 59 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 9121 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) : 0.7151179 object centre at (A) : 20.78350 0.8889999 10.83300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3929229E-02 9.9415250E-02 midg,1,midg; midg,igrid,midg -3.0037090E-02 1.4819586E-02 1,midg,midg; igrid,midg,midg 5.6758703E-04 1.3484960E-02 gauss-seidel spectral radius is 0.9987867 estimated iterations to convergence 227 setup time was (sec) 0.7800000 now iterating at: 12:56:32 rms-change max change #iterations 3.609941 204.4592 at 10iterations 1.751814 78.46809 at 20iterations 0.8520505 33.00414 at 30iterations 0.4160573 16.00549 at 40iterations 0.2030016 7.943459 at 50iterations 9.9255741E-02 3.679022 at 60iterations 4.8317157E-02 1.845887 at 70iterations 2.3528790E-02 0.8474426 at 80iterations 1.1533638E-02 0.4153118 at 90iterations 5.6090811E-03 0.2076550 at 100iterations 2.7398542E-03 0.1178398 at 110iterations 1.3425534E-03 4.5944214E-02 at 120iterations finished qdiffx linear iterations at : 12:56:40 total time elapsed so far: 9.040000 # loops : 120 mean,max change (kT/e) : 1.3425534E-03 4.5944214E-02 energy calculations done at 9.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.220000 DelPhi exited at 12:56:40 9.226u 0.304s 0:09.80 97.1% 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 Sat Oct 8 2011 at 12:56:41 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1282 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.218030 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): -0.8800000 42.44700 ymin,ymax (A): -18.52500 20.30300 zmin,zma (A): -14.05800 35.72400 x,y,z range (A): 43.32700 38.82800 49.78200 scale (grids/A): 3.218030 object centre (A): 20.78350 0.8889999 10.83300 number of atom coordinates read : 1282 total number of charged atoms : 1147 net assigned charge : 2.000010 assigned positive charge : 189.4882 centred at (gu) : 89.20094 87.42953 90.96945 assigned negative charge : -187.4880 centred at (gu) : 89.35305 86.44379 88.90434 start vw surface at 0.1300000 fill in re-entrant regions at 0.6800000 boundary points on vw surface= 108124 reading accessible surface arcs data from file ARCDAT no. of arc points read = 13222 grid for indexing accessible points = 1.400000 m= 52647 mr = 72390 m= 21462 mr = 41771 m= 6760 mr = 16917 m= 1546 mr = 5039 m= 171 mr = 1035 m= 9 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.450000 number of dielectric boundary points 53507 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.590000 number of grid points assigned charge 9176 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) : 2.145354 object centre at (A) : 20.78350 0.8889999 10.83300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3368184 1.023548 midg,1,midg; midg,igrid,midg -0.2804560 0.1307421 1,midg,midg; igrid,midg,midg -4.4458319E-02 0.1201572 gauss-seidel spectral radius is 0.9992827 estimated iterations to convergence 295 setup time was (sec) 1.770000 now iterating at: 12:56:43 rms-change max change #iterations 8.102554 349.4080 at 10iterations 4.721813 121.4746 at 20iterations 2.737568 72.52022 at 30iterations 1.590898 37.80540 at 40iterations 0.9199514 25.39631 at 50iterations 0.5339568 13.12344 at 60iterations 0.3098643 7.322909 at 70iterations 0.1786005 3.879294 at 80iterations 0.1037616 2.503195 at 90iterations 5.9965082E-02 1.299683 at 100iterations 3.4780532E-02 0.7857661 at 110iterations 2.0040076E-02 0.4404147 at 120iterations 1.1561787E-02 0.2232590 at 130iterations 6.7147352E-03 0.1598971 at 140iterations 3.8897933E-03 8.1176758E-02 at 150iterations 2.2444332E-03 5.2585602E-02 at 160iterations 1.2992391E-03 2.7008057E-02 at 170iterations 7.5488375E-04 1.6034245E-02 at 180iterations finished qdiffx linear iterations at : 12:56:56 total time elapsed so far: 15.14000 # loops : 180 mean,max change (kT/e) : 7.5488375E-04 1.6034245E-02 energy calculations done at 15.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.32000 DelPhi exited at 12:56:56 15.320u 0.317s 0:15.92 98.1% 0+0k 0+0io 0pf+0w