Tue Oct 11 00:28:07 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 Tue Oct 11 2011 at 00:28:07 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4040 !!! WARNING: GLM 762 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.4995159 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): 2.820000 65.68300 ymin,ymax (A): 7.930000 79.19901 zmin,zma (A): 17.46700 87.88600 x,y,z range (A): 62.86300 71.26900 70.41901 scale (grids/A): 0.4995159 object centre (A): 34.25150 43.56450 52.67650 number of atom coordinates read : 4040 total number of charged atoms : 3885 net assigned charge : 9.406045 assigned positive charge : 623.2681 centred at (gu) : 89.47166 90.45252 88.03603 assigned negative charge : -613.8648 centred at (gu) : 89.39504 90.61076 88.09980 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 6369 nv = 96 ne = 84 npr = 79224 no. pairs analyzed = 79224 no. exposed pairs = 5215 no. arc points = 36275 no. surface atoms = 1759 nbur = 2281 mkacc time = 0.1900000 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 = 1.708000 m= 208 mr = 3123 m= 0 mr = 4 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 14 time to turn everything in is 0.4400000 number of dielectric boundary points 3450 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3558 ## 570 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 8594 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.8332686E-10 -3.4702889E-12 midg,1,midg; midg,igrid,midg 2.5832186E-10 -1.5987951E-10 1,midg,midg; igrid,midg,midg -3.0203184E-11 1.5956304E-10 gauss-seidel spectral radius is 0.9794593 estimated iterations to convergence 58 setup time was (sec) 0.6700000 now iterating at: 00:28:08 rms-change max change #iterations 5.7898171E-02 9.351885 at 10iterations 3.6125705E-03 0.7178802 at 20iterations 4.8238819E-04 0.1283226 at 30iterations 9.4969400E-05 2.7019501E-02 at 40iterations 1.9545392E-05 5.6457520E-03 at 50iterations finished qdiffx linear iterations at : 00:28:11 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 1.9545392E-05 5.6457520E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 00:28:13 3.529u 0.147s 0:05.55 65.9% 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 Tue Oct 11 2011 at 00:28:13 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4040 !!! WARNING: GLM 762 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.498548 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): 2.820000 65.68300 ymin,ymax (A): 7.930000 79.19901 zmin,zma (A): 17.46700 87.88600 x,y,z range (A): 62.86300 71.26900 70.41901 scale (grids/A): 1.498548 object centre (A): 34.25150 43.56450 52.67650 number of atom coordinates read : 4040 total number of charged atoms : 3885 net assigned charge : 9.406045 assigned positive charge : 623.2681 centred at (gu) : 88.41380 91.35636 84.10683 assigned negative charge : -613.8648 centred at (gu) : 88.18516 91.83202 84.29892 start vw surface at 0.2300000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 71837 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36275 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.624000 m= 19569 mr = 47416 m= 1483 mr = 12879 m= 22 mr = 607 m= 0 mr = 1 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1497 time to turn everything in is 0.6000000 number of dielectric boundary points 32008 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 473 ## 8 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 28918 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) : 0.4995159 object centre at (A) : 34.25150 43.56450 52.67650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.8145181E-03 -2.5566399E-02 midg,1,midg; midg,igrid,midg 2.8052565E-02 1.3740338E-02 1,midg,midg; igrid,midg,midg 3.0857313E-03 5.3337906E-03 gauss-seidel spectral radius is 0.9979258 estimated iterations to convergence 175 setup time was (sec) 0.9000000 now iterating at: 00:28:14 rms-change max change #iterations 3.293797 152.6956 at 10iterations 1.286093 49.68866 at 20iterations 0.5049028 19.26451 at 30iterations 0.1989531 7.354488 at 40iterations 7.7946857E-02 2.701790 at 50iterations 3.0689277E-02 1.265862 at 60iterations 1.2203176E-02 0.4082108 at 70iterations 4.9092756E-03 0.1815796 at 80iterations 2.0324197E-03 8.6158752E-02 at 90iterations 8.8818005E-04 4.0618896E-02 at 100iterations 4.1481786E-04 2.2216797E-02 at 110iterations 2.1251950E-04 1.2317657E-02 at 120iterations finished qdiffx linear iterations at : 00:28:21 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 2.1251950E-04 1.2317657E-02 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.810000 DelPhi exited at 00:28:22 7.810u 0.233s 0:08.77 91.6% 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 Tue Oct 11 2011 at 00:28:22 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: 303 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4040 !!! WARNING: GLM 762 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.247822 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): 2.820000 65.68300 ymin,ymax (A): 7.930000 79.19901 zmin,zma (A): 17.46700 87.88600 x,y,z range (A): 62.86300 71.26900 70.41901 scale (grids/A): 2.247822 object centre (A): 34.25150 43.56450 52.67650 number of atom coordinates read : 4040 total number of charged atoms : 3885 net assigned charge : 9.406045 assigned positive charge : 623.2681 centred at (gu) : 87.62028 92.03436 81.16003 assigned negative charge : -613.8648 centred at (gu) : 87.27770 92.74795 81.44840 start vw surface at 0.2200000 fill in re-entrant regions at 0.4700000 boundary points on vw surface= 167777 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36275 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.596000 m= 71183 mr = 117564 m= 16995 mr = 54851 m= 2017 mr = 12242 m= 50 mr = 1155 m= 0 mr = 12 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 4902 time to turn everything in is 1.330000 number of dielectric boundary points 72198 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 78 iepsmp to db, and charging done at 1.480000 number of grid points assigned charge 30973 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) : 1.498548 object centre at (A) : 34.25150 43.56450 52.67650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.4085242E-02 -0.4248903 midg,1,midg; midg,igrid,midg 0.4909752 0.2616203 1,midg,midg; igrid,midg,midg 0.1421694 0.1383624 gauss-seidel spectral radius is 0.9990742 estimated iterations to convergence 260 setup time was (sec) 1.660000 now iterating at: 00:28:24 rms-change max change #iterations 9.104543 290.2370 at 10iterations 5.041540 126.2160 at 20iterations 2.779641 74.24988 at 30iterations 1.516398 37.32093 at 40iterations 0.8267936 20.90305 at 50iterations 0.4493156 10.22802 at 60iterations 0.2431200 5.366463 at 70iterations 0.1314434 3.101053 at 80iterations 7.0867576E-02 1.715836 at 90iterations 3.8366370E-02 0.9575157 at 100iterations 2.0694278E-02 0.4507890 at 110iterations 1.1176238E-02 0.2463884 at 120iterations 6.0239262E-03 0.1247978 at 130iterations 3.2763428E-03 6.7550659E-02 at 140iterations 1.7809072E-03 3.8704872E-02 at 150iterations 9.7527180E-04 2.2693634E-02 at 160iterations 5.4199831E-04 1.3652802E-02 at 170iterations 3.0743261E-04 7.5645447E-03 at 180iterations finished qdiffx linear iterations at : 00:28:35 total time elapsed so far: 12.99000 # loops : 180 mean,max change (kT/e) : 3.0743261E-04 7.5645447E-03 energy calculations done at 12.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.18000 DelPhi exited at 00:28:36 13.180u 0.233s 0:14.04 95.5% 0+0k 0+0io 0pf+0w