Sat Oct 15 15:40:24 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 15 2011 at 15:40:24 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2042 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: 0.7289107 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): -14.59300 34.24700 ymin,ymax (A): -22.24800 24.71400 zmin,zma (A): -13.55900 28.55300 x,y,z range (A): 48.84000 46.96200 42.11200 scale (grids/A): 0.7289107 object centre (A): 9.827001 1.233000 7.497000 number of atom coordinates read : 2042 total number of charged atoms : 1936 net assigned charge : 6.500009 assigned positive charge : 313.9360 centred at (gu) : 89.47188 89.05590 90.10706 assigned negative charge : -307.4362 centred at (gu) : 89.55465 89.16941 90.17840 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 7410 nv = 96 ne = 84 npr = 40655 no. pairs analyzed = 40655 no. exposed pairs = 2535 no. arc points = 17196 no. surface atoms = 860 nbur = 1182 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 550 mr = 4298 m= 3 mr = 105 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 0.1700000 number of dielectric boundary points 3560 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1542 ## 160 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 8074 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4065580E-07 3.3443662E-08 midg,1,midg; midg,igrid,midg 2.1002707E-07 4.9860965E-10 1,midg,midg; igrid,midg,midg 1.6813073E-07 2.2061668E-08 gauss-seidel spectral radius is 0.9901811 estimated iterations to convergence 82 setup time was (sec) 0.3700000 now iterating at: 15:40:24 rms-change max change #iterations 0.2263186 31.42629 at 10iterations 2.9396223E-02 4.396694 at 20iterations 4.0705996E-03 0.4965334 at 30iterations 6.3803670E-04 8.9046478E-02 at 40iterations 1.4570841E-04 1.9111633E-02 at 50iterations finished qdiffx linear iterations at : 15:40:28 total time elapsed so far: 3.500000 # loops : 50 mean,max change (kT/e) : 1.4570841E-04 1.9111633E-02 energy calculations done at 3.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.640000 DelPhi exited at 15:40:29 3.640u 0.189s 0:05.02 76.0% 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 15 2011 at 15:40:29 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2042 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: 2.186732 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): -14.59300 34.24700 ymin,ymax (A): -22.24800 24.71400 zmin,zma (A): -13.55900 28.55300 x,y,z range (A): 48.84000 46.96200 42.11200 scale (grids/A): 2.186732 object centre (A): 9.827001 1.233000 7.497000 number of atom coordinates read : 2042 total number of charged atoms : 1936 net assigned charge : 6.500009 assigned positive charge : 313.9360 centred at (gu) : 88.41565 87.16769 90.32111 assigned negative charge : -307.4362 centred at (gu) : 88.66412 87.50836 90.53531 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 78659 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17196 grid for indexing accessible points = 1.400000 m= 32242 mr = 55864 m= 6445 mr = 24721 m= 635 mr = 4321 m= 19 mr = 349 m= 0 mr = 3 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 32742 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 53 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 15390 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) : 0.7289107 object centre at (A) : 9.827001 1.233000 7.497000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5823383E-02 3.3616874E-02 midg,1,midg; midg,igrid,midg 5.5802204E-02 -5.7947442E-02 1,midg,midg; igrid,midg,midg 5.6370180E-02 3.9240319E-02 gauss-seidel spectral radius is 0.9988880 estimated iterations to convergence 237 setup time was (sec) 0.6700000 now iterating at: 15:40:30 rms-change max change #iterations 4.846574 215.0470 at 10iterations 2.435019 77.48235 at 20iterations 1.234347 43.56296 at 30iterations 0.6209763 17.10690 at 40iterations 0.3129043 9.548733 at 50iterations 0.1587059 4.520214 at 60iterations 8.0305912E-02 2.569302 at 70iterations 4.0395625E-02 1.236168 at 80iterations 2.0497693E-02 0.5749769 at 90iterations 1.0420182E-02 0.3095341 at 100iterations 5.3356499E-03 0.1531525 at 110iterations 2.7522673E-03 8.2694352E-02 at 120iterations finished qdiffx linear iterations at : 15:40:40 total time elapsed so far: 8.170000 # loops : 120 mean,max change (kT/e) : 2.7522673E-03 8.2694352E-02 energy calculations done at 8.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.300000 DelPhi exited at 15:40:40 8.299u 0.265s 0:11.52 74.2% 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 15 2011 at 15:40:40 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2042 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: 3.280098 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): -14.59300 34.24700 ymin,ymax (A): -22.24800 24.71400 zmin,zma (A): -13.55900 28.55300 x,y,z range (A): 48.84000 46.96200 42.11200 scale (grids/A): 3.280098 object centre (A): 9.827001 1.233000 7.497000 number of atom coordinates read : 2042 total number of charged atoms : 1936 net assigned charge : 6.500009 assigned positive charge : 313.9360 centred at (gu) : 87.62336 85.75137 90.48177 assigned negative charge : -307.4362 centred at (gu) : 87.99623 86.26263 90.80307 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 181085 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17196 grid for indexing accessible points = 1.400000 m= 99872 mr = 134465 m= 41435 mr = 83467 m= 12245 mr = 34312 m= 2470 mr = 9566 m= 372 mr = 1760 m= 11 mr = 257 m= 0 mr = 5 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.290000 number of dielectric boundary points 73658 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.420000 number of grid points assigned charge 15488 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) : 2.186732 object centre at (A) : 9.827001 1.233000 7.497000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1191009 0.2786967 midg,1,midg; midg,igrid,midg 0.4967566 -0.6757618 1,midg,midg; igrid,midg,midg 0.4250212 0.2647848 gauss-seidel spectral radius is 0.9993111 estimated iterations to convergence 301 setup time was (sec) 1.570000 now iterating at: 15:40:43 rms-change max change #iterations 10.61382 330.0624 at 10iterations 6.317914 121.9628 at 20iterations 3.753610 75.72618 at 30iterations 2.227024 43.60166 at 40iterations 1.319895 27.11833 at 50iterations 0.7784610 14.20772 at 60iterations 0.4600325 8.535129 at 70iterations 0.2720317 4.840954 at 80iterations 0.1603801 2.933792 at 90iterations 9.4689026E-02 1.783477 at 100iterations 5.5948965E-02 0.8786268 at 110iterations 3.3128012E-02 0.5655003 at 120iterations 1.9675046E-02 0.3853493 at 130iterations 1.1852418E-02 0.2115479 at 140iterations 7.2685662E-03 0.1221371 at 150iterations 4.5971321E-03 8.6059570E-02 at 160iterations 3.0323095E-03 5.8216095E-02 at 170iterations 2.1243934E-03 3.8211823E-02 at 180iterations finished qdiffx linear iterations at : 15:40:59 total time elapsed so far: 13.94000 # loops : 180 mean,max change (kT/e) : 2.1243934E-03 3.8211823E-02 energy calculations done at 13.94000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.06000 DelPhi exited at 15:41:00 14.061u 0.280s 0:19.68 72.8% 0+0k 0+0io 0pf+0w