Sun Oct 9 16:10:09 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 16:10:09 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3069 !!! WARNING: GLM 226 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6336098 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): -16.04900 36.76700 ymin,ymax (A): 55.69100 108.2790 zmin,zma (A): -5.245000 50.94100 x,y,z range (A): 52.81600 52.58800 56.18600 scale (grids/A): 0.6336098 object centre (A): 10.35900 81.98500 22.84800 number of atom coordinates read : 3069 total number of charged atoms : 2920 net assigned charge : -5.593981 assigned positive charge : 453.5971 centred at (gu) : 90.45887 88.76833 91.50491 assigned negative charge : -459.1925 centred at (gu) : 90.47320 88.65586 91.56031 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8093 nv = 96 ne = 84 npr = 63902 no. pairs analyzed = 63902 no. exposed pairs = 3685 no. arc points = 25809 no. surface atoms = 1251 nbur = 1818 mkacc time = 0.1700000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 494 mr = 4492 m= 4 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 10 time to turn everything in is 0.3800000 number of dielectric boundary points 4020 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2498 ## 213 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 9951 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4994880E-10 -1.7796156E-08 midg,1,midg; midg,igrid,midg -2.5574098E-08 4.7896891E-09 1,midg,midg; igrid,midg,midg -4.3600261E-09 -8.9093266E-09 gauss-seidel spectral radius is 0.9871358 estimated iterations to convergence 72 setup time was (sec) 0.6600000 now iterating at: 16:10:10 rms-change max change #iterations 0.1523556 20.88781 at 10iterations 1.5005106E-02 1.833929 at 20iterations 1.4545101E-03 0.1847086 at 30iterations 1.4739738E-04 1.9535065E-02 at 40iterations 1.6834898E-05 2.3765564E-03 at 50iterations finished qdiffx linear iterations at : 16:10:14 total time elapsed so far: 3.940000 # loops : 50 mean,max change (kT/e) : 1.6834898E-05 2.3765564E-03 energy calculations done at 3.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.110000 DelPhi exited at 16:10:14 4.113u 0.270s 0:04.64 94.3% 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 16:10:14 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3069 !!! WARNING: GLM 226 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.900829 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): -16.04900 36.76700 ymin,ymax (A): 55.69100 108.2790 zmin,zma (A): -5.245000 50.94100 x,y,z range (A): 52.81600 52.58800 56.18600 scale (grids/A): 1.900829 object centre (A): 10.35900 81.98500 22.84800 number of atom coordinates read : 3069 total number of charged atoms : 2920 net assigned charge : -5.593981 assigned positive charge : 453.5971 centred at (gu) : 91.37609 86.30425 94.51386 assigned negative charge : -459.1925 centred at (gu) : 91.41947 85.96726 94.68063 start vw surface at 0.1800000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 86848 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25809 grid for indexing accessible points = 1.400000 m= 32089 mr = 60562 m= 5774 mr = 23560 m= 361 mr = 3762 m= 4 mr = 122 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 914 time to turn everything in is 0.7800000 number of dielectric boundary points 37070 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 165 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 22967 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) : 0.6336098 object centre at (A) : 10.35900 81.98500 22.84800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0683799E-02 1.7403161E-02 midg,1,midg; midg,igrid,midg -4.0500190E-02 -1.6214203E-02 1,midg,midg; igrid,midg,midg -2.2474313E-02 -4.1960791E-02 gauss-seidel spectral radius is 0.9986678 estimated iterations to convergence 217 setup time was (sec) 1.080000 now iterating at: 16:10:15 rms-change max change #iterations 4.651885 167.0590 at 10iterations 2.192517 75.29544 at 20iterations 1.035038 34.59791 at 30iterations 0.4879277 14.84143 at 40iterations 0.2316242 7.228090 at 50iterations 0.1096537 3.184357 at 60iterations 5.1709041E-02 1.489866 at 70iterations 2.4408385E-02 0.7153435 at 80iterations 1.1570168E-02 0.3390236 at 90iterations 5.4606777E-03 0.1582842 at 100iterations 2.5855270E-03 7.7194214E-02 at 110iterations 1.2278999E-03 3.4013271E-02 at 120iterations finished qdiffx linear iterations at : 16:10:24 total time elapsed so far: 9.470000 # loops : 120 mean,max change (kT/e) : 1.2278999E-03 3.4013271E-02 energy calculations done at 9.470000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.660000 DelPhi exited at 16:10:24 9.658u 0.291s 0:10.21 97.3% 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 16:10:24 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3069 !!! WARNING: GLM 226 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.851244 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): -16.04900 36.76700 ymin,ymax (A): 55.69100 108.2790 zmin,zma (A): -5.245000 50.94100 x,y,z range (A): 52.81600 52.58800 56.18600 scale (grids/A): 2.851244 object centre (A): 10.35900 81.98500 22.84800 number of atom coordinates read : 3069 total number of charged atoms : 2920 net assigned charge : -5.593981 assigned positive charge : 453.5971 centred at (gu) : 92.06379 84.45609 96.77052 assigned negative charge : -459.1925 centred at (gu) : 92.12912 83.95076 97.02087 start vw surface at 0.1600000 fill in re-entrant regions at 0.6500000 boundary points on vw surface= 201171 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25809 grid for indexing accessible points = 1.400000 m= 101857 mr = 147078 m= 39366 mr = 83080 m= 10689 mr = 31661 m= 1619 mr = 8256 m= 87 mr = 1082 m= 1 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 1.240000 no. cavity mid-points inaccessible to solvent = 2953 time to turn everything in is 2.010000 number of dielectric boundary points 83604 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 2.170000 number of grid points assigned charge 23354 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) : 1.900829 object centre at (A) : 10.35900 81.98500 22.84800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4544516 0.2966382 midg,1,midg; midg,igrid,midg -0.3580236 -0.3056769 1,midg,midg; igrid,midg,midg -0.2562009 -0.4471018 gauss-seidel spectral radius is 0.9992779 estimated iterations to convergence 294 setup time was (sec) 2.340000 now iterating at: 16:10:27 rms-change max change #iterations 10.93140 438.6195 at 10iterations 6.447677 132.5400 at 20iterations 3.781732 87.77766 at 30iterations 2.215848 39.06894 at 40iterations 1.291636 24.62425 at 50iterations 0.7535849 13.96244 at 60iterations 0.4380612 7.910306 at 70iterations 0.2546616 4.238056 at 80iterations 0.1479021 2.512867 at 90iterations 8.5654423E-02 1.577003 at 100iterations 4.9701661E-02 0.8965492 at 110iterations 2.8828451E-02 0.4970245 at 120iterations 1.6685678E-02 0.2797626 at 130iterations 9.6796658E-03 0.1703434 at 140iterations 5.6026955E-03 0.1027069 at 150iterations 3.2470308E-03 5.8402538E-02 at 160iterations 1.8796908E-03 3.3796310E-02 at 170iterations 1.0881760E-03 1.9196510E-02 at 180iterations finished qdiffx linear iterations at : 16:10:41 total time elapsed so far: 16.34000 # loops : 180 mean,max change (kT/e) : 1.0881760E-03 1.9196510E-02 energy calculations done at 16.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.52000 DelPhi exited at 16:10:41 16.519u 0.342s 0:17.11 98.4% 0+0k 0+0io 0pf+0w