Mon Oct 10 14:01:24 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+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 Mon Oct 10 2011 at 14:01:24 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6217 !!! WARNING: HIR 702 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 0.4641097 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): 3.671000 80.37700 ymin,ymax (A): 22.07600 85.61200 zmin,zma (A): 6.338000 70.59400 x,y,z range (A): 76.70600 63.53600 64.25600 scale (grids/A): 0.4641097 object centre (A): 42.02400 53.84400 38.46600 number of atom coordinates read : 6217 total number of charged atoms : 6049 net assigned charge : -3.985977 assigned positive charge : 941.0012 centred at (gu) : 89.89877 88.84440 89.27225 assigned negative charge : -944.9955 centred at (gu) : 89.82512 88.86467 89.16301 start vw surface at 0.2100000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 8162 nv = 96 ne = 84 npr = 126024 no. pairs analyzed = 126024 no. exposed pairs = 7715 no. arc points = 53169 no. surface atoms = 2595 nbur = 3622 mkacc time = 0.2600000 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 = 1.848000 m= 244 mr = 4128 m= 2 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 4280 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4937 ## 953 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 11237 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.9632355E-11 2.9007690E-11 midg,1,midg; midg,igrid,midg 3.3285972E-12 -9.5762712E-12 1,midg,midg; igrid,midg,midg -3.5160680E-11 2.1892654E-11 gauss-seidel spectral radius is 0.9763817 estimated iterations to convergence 54 setup time was (sec) 0.7700000 now iterating at: 14:01:25 rms-change max change #iterations 4.7123108E-02 7.366798 at 10iterations 2.2185529E-03 0.3382835 at 20iterations 2.4857747E-04 6.6883087E-02 at 30iterations 5.9988957E-05 1.6084671E-02 at 40iterations 1.6834440E-05 4.1675568E-03 at 50iterations finished qdiffx linear iterations at : 14:01:28 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 1.6834440E-05 4.1675568E-03 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 14:01:29 3.472u 0.180s 0:04.97 73.4% 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 Mon Oct 10 2011 at 14:01:29 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6217 !!! WARNING: HIR 702 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.392329 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): 3.671000 80.37700 ymin,ymax (A): 22.07600 85.61200 zmin,zma (A): 6.338000 70.59400 x,y,z range (A): 76.70600 63.53600 64.25600 scale (grids/A): 1.392329 object centre (A): 42.02400 53.84400 38.46600 number of atom coordinates read : 6217 total number of charged atoms : 6049 net assigned charge : -3.985977 assigned positive charge : 941.0012 centred at (gu) : 89.69410 86.53122 87.81487 assigned negative charge : -944.9955 centred at (gu) : 89.47496 86.59364 87.48884 start vw surface at 0.2200000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 94338 reading accessible surface arcs data from file ARCDAT no. of arc points read = 53169 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.736000 m= 23577 mr = 64139 m= 1351 mr = 14492 m= 10 mr = 401 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 961 time to turn everything in is 0.6900000 number of dielectric boundary points 40244 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 908 ## 22 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 43679 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) : 0.4641097 object centre at (A) : 42.02400 53.84400 38.46600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.9776624E-03 4.3077883E-03 midg,1,midg; midg,igrid,midg -1.6084616E-03 -2.3072201E-03 1,midg,midg; igrid,midg,midg -6.7852661E-03 -5.4122745E-03 gauss-seidel spectral radius is 0.9977883 estimated iterations to convergence 169 setup time was (sec) 0.9700000 now iterating at: 14:01:30 rms-change max change #iterations 3.522359 167.5213 at 10iterations 1.338000 41.89037 at 20iterations 0.5125987 17.45037 at 30iterations 0.1958028 6.933487 at 40iterations 7.4828364E-02 2.647003 at 50iterations 2.8596470E-02 0.9774055 at 60iterations 1.0987648E-02 0.3624821 at 70iterations 4.1985540E-03 0.1368790 at 80iterations 1.6156998E-03 5.3697586E-02 at 90iterations 6.2671048E-04 2.2295952E-02 at 100iterations 2.4859718E-04 9.4211698E-03 at 110iterations 1.0313053E-04 3.7002563E-03 at 120iterations finished qdiffx linear iterations at : 14:01:36 total time elapsed so far: 7.200000 # loops : 120 mean,max change (kT/e) : 1.0313053E-04 3.7002563E-03 energy calculations done at 7.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.380000 DelPhi exited at 14:01:37 7.382u 0.200s 0:07.94 95.4% 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 Mon Oct 10 2011 at 14:01:37 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 6217 !!! WARNING: HIR 702 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1600000 grid size : 179 scale,in grids/A, set to be: 2.088494 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): 3.671000 80.37700 ymin,ymax (A): 22.07600 85.61200 zmin,zma (A): 6.338000 70.59400 x,y,z range (A): 76.70600 63.53600 64.25600 scale (grids/A): 2.088494 object centre (A): 42.02400 53.84400 38.46600 number of atom coordinates read : 6217 total number of charged atoms : 6049 net assigned charge : -3.985977 assigned positive charge : 941.0012 centred at (gu) : 89.54072 84.79625 86.72189 assigned negative charge : -944.9955 centred at (gu) : 89.21231 84.89070 86.23329 start vw surface at 0.2500000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 221004 reading accessible surface arcs data from file ARCDAT no. of arc points read = 53169 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.708000 m= 90274 mr = 159044 m= 17832 mr = 68086 m= 1601 mr = 11814 m= 32 mr = 750 m= 0 mr = 6 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 3243 time to turn everything in is 1.540000 number of dielectric boundary points 91043 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 184 iepsmp to db, and charging done at 1.670000 number of grid points assigned charge 48012 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) : 1.392329 object centre at (A) : 42.02400 53.84400 38.46600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.0574257E-02 5.9615713E-02 midg,1,midg; midg,igrid,midg -1.5005329E-02 -2.9315997E-02 1,midg,midg; igrid,midg,midg -2.5673267E-02 -0.5383242 gauss-seidel spectral radius is 0.9990992 estimated iterations to convergence 263 setup time was (sec) 1.820000 now iterating at: 14:01:39 rms-change max change #iterations 10.30646 283.9098 at 10iterations 5.831800 142.8257 at 20iterations 3.279702 73.97771 at 30iterations 1.826799 50.04391 at 40iterations 1.015309 23.37021 at 50iterations 0.5622580 12.02370 at 60iterations 0.3102889 7.647629 at 70iterations 0.1711137 3.916420 at 80iterations 9.4045237E-02 1.875896 at 90iterations 5.1550373E-02 0.9787407 at 100iterations 2.8299792E-02 0.5331554 at 110iterations 1.5497456E-02 0.3148219 at 120iterations 8.4825745E-03 0.1699638 at 130iterations 4.6376698E-03 8.7860107E-02 at 140iterations 2.5380640E-03 4.9210548E-02 at 150iterations 1.3871555E-03 2.8554440E-02 at 160iterations 7.6058606E-04 1.4432788E-02 at 170iterations 4.1769719E-04 8.5945129E-03 at 180iterations finished qdiffx linear iterations at : 14:01:51 total time elapsed so far: 13.85000 # loops : 180 mean,max change (kT/e) : 4.1769719E-04 8.5945129E-03 energy calculations done at 13.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.05000 DelPhi exited at 14:01:52 14.047u 0.231s 0:14.83 96.2% 0+0k 0+0io 0pf+0w