Sun Oct 9 13:45:31 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 Sun Oct 9 2011 at 13:45:31 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2333 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: 0.6905247 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): -7.055000 44.50000 ymin,ymax (A): -14.02800 35.33700 zmin,zma (A): 1.882000 45.89400 x,y,z range (A): 51.55500 49.36500 44.01200 scale (grids/A): 0.6905247 object centre (A): 18.72250 10.65450 23.88800 number of atom coordinates read : 2333 total number of charged atoms : 2195 net assigned charge : 6.500011 assigned positive charge : 356.1172 centred at (gu) : 89.65870 91.58551 90.49578 assigned negative charge : -349.6176 centred at (gu) : 89.66853 91.64047 90.56126 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 7584 nv = 96 ne = 84 npr = 46429 no. pairs analyzed = 46429 no. exposed pairs = 2980 no. arc points = 20986 no. surface atoms = 999 nbur = 1334 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 466 mr = 4158 m= 3 mr = 77 m= 0 mr = 0 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3818 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1959 ## 192 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 8522 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.5554118E-08 1.3135526E-08 midg,1,midg; midg,igrid,midg 4.2113399E-08 2.1332728E-08 1,midg,midg; igrid,midg,midg 4.3281421E-08 3.1041399E-08 gauss-seidel spectral radius is 0.9891023 estimated iterations to convergence 78 setup time was (sec) 0.3700000 now iterating at: 13:45:32 rms-change max change #iterations 0.1962178 25.20667 at 10iterations 2.3285624E-02 3.340996 at 20iterations 3.3535066E-03 0.4350338 at 30iterations 8.0548890E-04 0.1305161 at 40iterations 2.7918062E-04 4.5509338E-02 at 50iterations finished qdiffx linear iterations at : 13:45:35 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 2.7918062E-04 4.5509338E-02 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 13:45:35 3.393u 0.175s 0:03.85 92.4% 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 Sun Oct 9 2011 at 13:45:35 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2333 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: 2.071574 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): -7.055000 44.50000 ymin,ymax (A): -14.02800 35.33700 zmin,zma (A): 1.882000 45.89400 x,y,z range (A): 51.55500 49.36500 44.01200 scale (grids/A): 2.071574 object centre (A): 18.72250 10.65450 23.88800 number of atom coordinates read : 2333 total number of charged atoms : 2195 net assigned charge : 6.500011 assigned positive charge : 356.1172 centred at (gu) : 88.97575 94.75636 91.48681 assigned negative charge : -349.6176 centred at (gu) : 89.00529 94.92134 91.68357 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 80765 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20986 grid for indexing accessible points = 1.400000 m= 30737 mr = 56044 m= 5411 mr = 22593 m= 482 mr = 3391 m= 12 mr = 244 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 35135 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 115 iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 17401 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) : 0.6905247 object centre at (A) : 18.72250 10.65450 23.88800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8298565E-02 1.4330480E-02 midg,1,midg; midg,igrid,midg 1.1840628E-02 8.4160063E-03 1,midg,midg; igrid,midg,midg 5.2087869E-02 -2.3982393E-02 gauss-seidel spectral radius is 0.9988154 estimated iterations to convergence 230 setup time was (sec) 0.6300000 now iterating at: 13:45:36 rms-change max change #iterations 4.733545 219.8216 at 10iterations 2.320232 69.40590 at 20iterations 1.145376 39.77607 at 30iterations 0.5672393 17.58253 at 40iterations 0.2783728 8.666939 at 50iterations 0.1378993 3.880404 at 60iterations 6.8351120E-02 2.032943 at 70iterations 3.3779763E-02 1.012863 at 80iterations 1.6908687E-02 0.4898014 at 90iterations 8.5229091E-03 0.2713356 at 100iterations 4.3883892E-03 0.1336479 at 110iterations 2.3604038E-03 7.8231812E-02 at 120iterations finished qdiffx linear iterations at : 13:45:43 total time elapsed so far: 7.760000 # loops : 120 mean,max change (kT/e) : 2.3604038E-03 7.8231812E-02 energy calculations done at 7.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.880000 DelPhi exited at 13:45:44 7.885u 0.192s 0:08.35 96.6% 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 Sun Oct 9 2011 at 13:45:44 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: 279 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2333 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: 3.107361 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): -7.055000 44.50000 ymin,ymax (A): -14.02800 35.33700 zmin,zma (A): 1.882000 45.89400 x,y,z range (A): 51.55500 49.36500 44.01200 scale (grids/A): 3.107361 object centre (A): 18.72250 10.65450 23.88800 number of atom coordinates read : 2333 total number of charged atoms : 2195 net assigned charge : 6.500011 assigned positive charge : 356.1172 centred at (gu) : 88.46350 97.13443 92.23014 assigned negative charge : -349.6176 centred at (gu) : 88.50793 97.38197 92.52539 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 186096 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20986 grid for indexing accessible points = 1.400000 m= 97398 mr = 135146 m= 37288 mr = 79592 m= 9965 mr = 29989 m= 1953 mr = 7474 m= 233 mr = 1371 m= 4 mr = 135 m= 0 mr = 0 time to grow re-entrant surface = 0.6200001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.220000 number of dielectric boundary points 79230 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.310000 number of grid points assigned charge 17559 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) : 2.071574 object centre at (A) : 18.72250 10.65450 23.88800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5308242 3.2620914E-02 midg,1,midg; midg,igrid,midg 0.2024140 1.2954034E-02 1,midg,midg; igrid,midg,midg 0.6250452 -0.6264212 gauss-seidel spectral radius is 0.9992979 estimated iterations to convergence 298 setup time was (sec) 1.450000 now iterating at: 13:45:45 rms-change max change #iterations 10.69616 409.1012 at 10iterations 6.375119 140.5839 at 20iterations 3.777919 75.82893 at 30iterations 2.233418 41.07321 at 40iterations 1.323358 23.43573 at 50iterations 0.7776101 17.54746 at 60iterations 0.4585074 7.669697 at 70iterations 0.2692358 4.755353 at 80iterations 0.1580466 2.635732 at 90iterations 9.2907347E-02 1.720732 at 100iterations 5.4571159E-02 0.9089689 at 110iterations 3.2169960E-02 0.5781860 at 120iterations 1.9126261E-02 0.3459053 at 130iterations 1.1578751E-02 0.2162590 at 140iterations 7.1794079E-03 0.1388969 at 150iterations 4.6609011E-03 0.1018276 at 160iterations 3.2152724E-03 6.6365719E-02 at 170iterations 2.3611924E-03 5.0056458E-02 at 180iterations finished qdiffx linear iterations at : 13:45:57 total time elapsed so far: 12.89000 # loops : 180 mean,max change (kT/e) : 2.3611924E-03 5.0056458E-02 energy calculations done at 12.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.03000 DelPhi exited at 13:45:57 13.034u 0.219s 0:13.51 98.0% 0+0k 0+0io 0pf+0w