Sat Oct 8 14:33:57 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 Sat Oct 8 2011 at 14:33:58 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2994 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NDP 318 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6390808 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): -12.14400 43.56100 ymin,ymax (A): -22.88300 22.33300 zmin,zma (A): -6.577000 47.75700 x,y,z range (A): 55.70500 45.21600 54.33400 scale (grids/A): 0.6390808 object centre (A): 15.70850 -0.2749996 20.59000 number of atom coordinates read : 2994 total number of charged atoms : 2849 net assigned charge : 1.014008 assigned positive charge : 449.7066 centred at (gu) : 88.81583 89.73639 91.45354 assigned negative charge : -448.6933 centred at (gu) : 88.73325 89.58991 91.43262 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8140 nv = 96 ne = 84 npr = 62741 no. pairs analyzed = 62741 no. exposed pairs = 3377 no. arc points = 23896 no. surface atoms = 1158 nbur = 1836 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 403 mr = 4734 m= 2 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.3100000 number of dielectric boundary points 3772 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2349 ## 222 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 9879 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -8.1282003E-10 5.9500347E-09 midg,1,midg; midg,igrid,midg -1.8960050E-08 1.9353385E-08 1,midg,midg; igrid,midg,midg -1.2110140E-08 9.5534487E-09 gauss-seidel spectral radius is 0.9873457 estimated iterations to convergence 73 setup time was (sec) 0.5900000 now iterating at: 14:33:58 rms-change max change #iterations 0.1541460 23.60283 at 10iterations 1.5233499E-02 1.819109 at 20iterations 1.5469355E-03 0.1904297 at 30iterations 1.5813035E-04 2.1275997E-02 at 40iterations 1.7633023E-05 2.3031235E-03 at 50iterations finished qdiffx linear iterations at : 14:34:02 total time elapsed so far: 4.020000 # loops : 50 mean,max change (kT/e) : 1.7633023E-05 2.3031235E-03 energy calculations done at 4.020000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.200000 DelPhi exited at 14:34:02 4.203u 0.249s 0:04.87 91.1% 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 14:34:02 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2994 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NDP 318 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.917243 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): -12.14400 43.56100 ymin,ymax (A): -22.88300 22.33300 zmin,zma (A): -6.577000 47.75700 x,y,z range (A): 55.70500 45.21600 54.33400 scale (grids/A): 1.917243 object centre (A): 15.70850 -0.2749996 20.59000 number of atom coordinates read : 2994 total number of charged atoms : 2849 net assigned charge : 1.014008 assigned positive charge : 449.7066 centred at (gu) : 86.44704 89.20876 94.35986 assigned negative charge : -448.6933 centred at (gu) : 86.19955 88.76942 94.29758 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 88555 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23896 grid for indexing accessible points = 1.400000 m= 31429 mr = 63742 m= 4465 mr = 23644 m= 253 mr = 2624 m= 3 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 388 time to turn everything in is 0.6300000 number of dielectric boundary points 34629 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 155 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 22430 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) : 0.6390808 object centre at (A) : 15.70850 -0.2749996 20.59000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5376327E-03 1.3265375E-02 midg,1,midg; midg,igrid,midg -8.7144878E-03 2.8335406E-02 1,midg,midg; igrid,midg,midg -5.4137021E-02 1.6938899E-02 gauss-seidel spectral radius is 0.9986855 estimated iterations to convergence 219 setup time was (sec) 0.9500000 now iterating at: 14:34:04 rms-change max change #iterations 4.674809 182.9815 at 10iterations 2.228137 78.29731 at 20iterations 1.058668 32.41341 at 30iterations 0.5042927 15.68188 at 40iterations 0.2398060 7.210225 at 50iterations 0.1139013 3.393475 at 60iterations 5.4069441E-02 1.588154 at 70iterations 2.5774762E-02 0.7691784 at 80iterations 1.2268461E-02 0.3494434 at 90iterations 5.8381194E-03 0.1822066 at 100iterations 2.7779443E-03 8.0340385E-02 at 110iterations 1.3264630E-03 4.0931702E-02 at 120iterations finished qdiffx linear iterations at : 14:34:12 total time elapsed so far: 9.530000 # loops : 120 mean,max change (kT/e) : 1.3264630E-03 4.0931702E-02 energy calculations done at 9.530000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.710000 DelPhi exited at 14:34:13 9.712u 0.293s 0:10.31 96.9% 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 14:34:13 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2994 !!! WARNING: HIR 110 has a net charge of 0.5140 !!! WARNING: NDP 318 has a net charge of -3.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.875864 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): -12.14400 43.56100 ymin,ymax (A): -22.88300 22.33300 zmin,zma (A): -6.577000 47.75700 x,y,z range (A): 55.70500 45.21600 54.33400 scale (grids/A): 2.875864 object centre (A): 15.70850 -0.2749996 20.59000 number of atom coordinates read : 2994 total number of charged atoms : 2849 net assigned charge : 1.014008 assigned positive charge : 449.7066 centred at (gu) : 84.67048 88.81295 96.53998 assigned negative charge : -448.6933 centred at (gu) : 84.29936 88.15400 96.44622 start vw surface at 0.1400000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 205187 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23896 grid for indexing accessible points = 1.400000 m= 103667 mr = 154147 m= 35886 mr = 86349 m= 7991 mr = 28787 m= 1105 mr = 5779 m= 71 mr = 705 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 1350 time to turn everything in is 1.660000 number of dielectric boundary points 78111 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.810000 number of grid points assigned charge 22791 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) : 1.917243 object centre at (A) : 15.70850 -0.2749996 20.59000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2072114E-02 0.2121648 midg,1,midg; midg,igrid,midg -6.6464774E-02 0.2953233 1,midg,midg; igrid,midg,midg -0.7232085 0.2084496 gauss-seidel spectral radius is 0.9992755 estimated iterations to convergence 293 setup time was (sec) 2.010000 now iterating at: 14:34:15 rms-change max change #iterations 10.87516 454.5283 at 10iterations 6.357009 122.6041 at 20iterations 3.699201 64.38394 at 30iterations 2.150599 35.30350 at 40iterations 1.245583 23.20889 at 50iterations 0.7220729 11.21293 at 60iterations 0.4181527 7.418304 at 70iterations 0.2420590 4.230464 at 80iterations 0.1399609 2.474587 at 90iterations 8.1036828E-02 1.433742 at 100iterations 4.6863936E-02 0.7982259 at 110iterations 2.7087010E-02 0.4635792 at 120iterations 1.5636211E-02 0.2517490 at 130iterations 9.0473220E-03 0.1583990 at 140iterations 5.2248202E-03 9.0209961E-02 at 150iterations 3.0194316E-03 5.2398682E-02 at 160iterations 1.7451830E-03 2.8930664E-02 at 170iterations 1.0099863E-03 1.7310143E-02 at 180iterations finished qdiffx linear iterations at : 14:34:29 total time elapsed so far: 15.81000 # loops : 180 mean,max change (kT/e) : 1.0099863E-03 1.7310143E-02 energy calculations done at 15.81000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.99000 DelPhi exited at 14:34:29 15.995u 0.292s 0:16.57 98.2% 0+0k 0+0io 0pf+0w