Sat Oct 8 14:04:32 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+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 Sat Oct 8 2011 at 14:04:32 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2999 !!! WARNING: NAP 316 has a net charge of -2.0000 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: 0.6417652 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): -12.18000 43.29200 ymin,ymax (A): -23.32000 22.29600 zmin,zma (A): -7.661000 47.21400 x,y,z range (A): 55.47200 45.61600 54.87500 scale (grids/A): 0.6417652 object centre (A): 15.55600 -0.5120001 19.77650 number of atom coordinates read : 2999 total number of charged atoms : 2891 net assigned charge : 7.1674585E-06 assigned positive charge : 454.2786 centred at (gu) : 88.73394 89.93373 91.80228 assigned negative charge : -454.2793 centred at (gu) : 88.72966 89.84726 91.71455 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8245 nv = 96 ne = 84 npr = 61852 no. pairs analyzed = 61852 no. exposed pairs = 3454 no. arc points = 24142 no. surface atoms = 1171 nbur = 1828 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 443 mr = 4817 m= 0 mr = 52 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2200000 number of dielectric boundary points 3819 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2316 ## 214 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 10035 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.7154257E-09 1.8086412E-08 midg,1,midg; midg,igrid,midg -1.2852316E-08 1.1815591E-08 1,midg,midg; igrid,midg,midg -1.1020356E-09 2.9330710E-10 gauss-seidel spectral radius is 0.9874508 estimated iterations to convergence 73 setup time was (sec) 0.4400000 now iterating at: 14:04:33 rms-change max change #iterations 0.1608738 20.72071 at 10iterations 1.6205778E-02 2.327177 at 20iterations 1.6744824E-03 0.2811012 at 30iterations 1.8669243E-04 2.4465561E-02 at 40iterations 2.5082330E-05 3.4694672E-03 at 50iterations finished qdiffx linear iterations at : 14:04:36 total time elapsed so far: 3.620000 # loops : 50 mean,max change (kT/e) : 2.5082330E-05 3.4694672E-03 energy calculations done at 3.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.750000 DelPhi exited at 14:04:36 3.755u 0.212s 0:04.27 92.7% 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 14:04:36 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2999 !!! WARNING: NAP 316 has a net charge of -2.0000 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: 1.925296 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): -12.18000 43.29200 ymin,ymax (A): -23.32000 22.29600 zmin,zma (A): -7.661000 47.21400 x,y,z range (A): 55.47200 45.61600 54.87500 scale (grids/A): 1.925296 object centre (A): 15.55600 -0.5120001 19.77650 number of atom coordinates read : 2999 total number of charged atoms : 2891 net assigned charge : 7.1674585E-06 assigned positive charge : 454.2786 centred at (gu) : 86.20121 89.80056 95.40630 assigned negative charge : -454.2793 centred at (gu) : 86.18906 89.54176 95.14349 start vw surface at 0.1100000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 89682 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24142 grid for indexing accessible points = 1.400000 m= 32730 mr = 64751 m= 4888 mr = 24747 m= 280 mr = 3024 m= 5 mr = 97 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 34966 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 168 iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 22781 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) : 0.6417652 object centre at (A) : 15.55600 -0.5120001 19.77650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5333984E-02 1.6268687E-02 midg,1,midg; midg,igrid,midg -2.2283355E-03 1.9303955E-02 1,midg,midg; igrid,midg,midg -3.5465114E-02 8.7553393E-03 gauss-seidel spectral radius is 0.9986954 estimated iterations to convergence 219 setup time was (sec) 0.7200000 now iterating at: 14:04:37 rms-change max change #iterations 4.735164 182.4702 at 10iterations 2.269053 65.39439 at 20iterations 1.080636 34.25945 at 30iterations 0.5159508 16.10884 at 40iterations 0.2460955 9.301907 at 50iterations 0.1171804 3.429386 at 60iterations 5.6021839E-02 1.708061 at 70iterations 2.6660684E-02 0.7999058 at 80iterations 1.2738333E-02 0.3378844 at 90iterations 6.0925740E-03 0.1757793 at 100iterations 2.8981443E-03 8.2992554E-02 at 110iterations 1.3874491E-03 4.0374756E-02 at 120iterations finished qdiffx linear iterations at : 14:04:46 total time elapsed so far: 8.940000 # loops : 120 mean,max change (kT/e) : 1.3874491E-03 4.0374756E-02 energy calculations done at 8.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.070000 DelPhi exited at 14:04:46 9.073u 0.252s 0:09.68 96.2% 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 14:04:46 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2999 !!! WARNING: NAP 316 has a net charge of -2.0000 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: 2.887944 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): -12.18000 43.29200 ymin,ymax (A): -23.32000 22.29600 zmin,zma (A): -7.661000 47.21400 x,y,z range (A): 55.47200 45.61600 54.87500 scale (grids/A): 2.887944 object centre (A): 15.55600 -0.5120001 19.77650 number of atom coordinates read : 2999 total number of charged atoms : 2891 net assigned charge : 7.1674585E-06 assigned positive charge : 454.2786 centred at (gu) : 84.30167 89.70071 98.10926 assigned negative charge : -454.2793 centred at (gu) : 84.28338 89.31261 97.71516 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.4000000 boundary points on vw surface= 207972 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24142 grid for indexing accessible points = 1.400000 m= 107382 mr = 156402 m= 37944 mr = 89783 m= 8830 mr = 30847 m= 1199 mr = 6519 m= 53 mr = 805 m= 1 mr = 14 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.160000 number of dielectric boundary points 79011 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.290000 number of grid points assigned charge 23128 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) : 1.925296 object centre at (A) : 15.55600 -0.5120001 19.77650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.1552471E-02 0.2614034 midg,1,midg; midg,igrid,midg -1.8752355E-02 0.2213643 1,midg,midg; igrid,midg,midg -0.4912308 0.1159852 gauss-seidel spectral radius is 0.9992788 estimated iterations to convergence 294 setup time was (sec) 1.450000 now iterating at: 14:04:48 rms-change max change #iterations 11.01327 396.6312 at 10iterations 6.480433 139.3786 at 20iterations 3.783240 76.64137 at 30iterations 2.209146 42.48355 at 40iterations 1.283893 23.02920 at 50iterations 0.7485130 13.11375 at 60iterations 0.4348594 7.622923 at 70iterations 0.2524000 4.269045 at 80iterations 0.1466857 2.590179 at 90iterations 8.4952518E-02 1.613736 at 100iterations 4.9266435E-02 0.8672094 at 110iterations 2.8562687E-02 0.4695091 at 120iterations 1.6548527E-02 0.2727640 at 130iterations 9.5996307E-03 0.1627579 at 140iterations 5.5645313E-03 0.1058254 at 150iterations 3.2370947E-03 5.0402164E-02 at 160iterations 1.8816971E-03 3.2529831E-02 at 170iterations 1.1006630E-03 1.9395828E-02 at 180iterations finished qdiffx linear iterations at : 14:05:01 total time elapsed so far: 14.91000 # loops : 180 mean,max change (kT/e) : 1.1006630E-03 1.9395828E-02 energy calculations done at 14.91000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.04000 DelPhi exited at 14:05:02 15.038u 0.315s 0:15.64 98.0% 0+0k 0+0io 0pf+0w