Sat Oct 8 14:36:11 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 8 2011 at 14:36:11 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3009 !!! WARNING: GLU 313 has a net charge of -0.2720 !!! 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6324279 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): -32.10300 24.18800 ymin,ymax (A): -22.98700 23.71700 zmin,zma (A): -11.29700 42.89300 x,y,z range (A): 56.29100 46.70400 54.19000 scale (grids/A): 0.6324279 object centre (A): -3.957500 0.3649998 15.79800 number of atom coordinates read : 3009 total number of charged atoms : 2864 net assigned charge : 1.728008 assigned positive charge : 451.0046 centred at (gu) : 91.59718 89.99979 88.85517 assigned negative charge : -449.2773 centred at (gu) : 91.58128 90.15227 88.80975 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 7844 nv = 96 ne = 84 npr = 63276 no. pairs analyzed = 63276 no. exposed pairs = 3389 no. arc points = 23897 no. surface atoms = 1149 nbur = 1860 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 395 mr = 4533 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3673 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2373 ## 237 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 9767 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.8067283E-09 5.4614038E-09 midg,1,midg; midg,igrid,midg 1.8424581E-08 -1.4866259E-08 1,midg,midg; igrid,midg,midg 2.5219610E-10 5.3564935E-09 gauss-seidel spectral radius is 0.9870785 estimated iterations to convergence 72 setup time was (sec) 0.5300000 now iterating at: 14:36:11 rms-change max change #iterations 0.1525481 22.89216 at 10iterations 1.4793905E-02 1.937416 at 20iterations 1.4841044E-03 0.1831932 at 30iterations 1.5629362E-04 2.0538807E-02 at 40iterations 1.9526322E-05 2.6826859E-03 at 50iterations finished qdiffx linear iterations at : 14:36:14 total time elapsed so far: 2.960000 # loops : 50 mean,max change (kT/e) : 1.9526322E-05 2.6826859E-03 energy calculations done at 2.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.130000 DelPhi exited at 14:36:15 3.138u 0.157s 0:03.70 88.6% 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 Sat Oct 8 2011 at 14:36:15 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3009 !!! WARNING: GLU 313 has a net charge of -0.2720 !!! 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.897284 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): -32.10300 24.18800 ymin,ymax (A): -22.98700 23.71700 zmin,zma (A): -11.29700 42.89300 x,y,z range (A): 56.29100 46.70400 54.19000 scale (grids/A): 1.897284 object centre (A): -3.957500 0.3649998 15.79800 number of atom coordinates read : 3009 total number of charged atoms : 2864 net assigned charge : 1.728008 assigned positive charge : 451.0046 centred at (gu) : 94.79069 89.99876 86.56477 assigned negative charge : -449.2773 centred at (gu) : 94.74346 90.45630 86.42891 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 86218 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23897 grid for indexing accessible points = 1.400000 m= 30555 mr = 61973 m= 4426 mr = 22882 m= 266 mr = 2717 m= 2 mr = 110 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 189 time to turn everything in is 0.5700000 number of dielectric boundary points 33785 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 150 iepsmp to db, and charging done at 0.6800000 number of grid points assigned charge 22523 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) : 0.6324279 object centre at (A) : -3.957500 0.3649998 15.79800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8243311E-02 1.2976757E-02 midg,1,midg; midg,igrid,midg 2.6882948E-02 -4.2714034E-03 1,midg,midg; igrid,midg,midg -4.1540363E-03 8.9493115E-03 gauss-seidel spectral radius is 0.9986577 estimated iterations to convergence 216 setup time was (sec) 0.8300000 now iterating at: 14:36:16 rms-change max change #iterations 4.599292 180.9729 at 10iterations 2.170529 75.78166 at 20iterations 1.024414 32.71247 at 30iterations 0.4823467 13.95715 at 40iterations 0.2274892 6.092896 at 50iterations 0.1074393 3.242194 at 60iterations 5.0779913E-02 1.511955 at 70iterations 2.3984708E-02 0.6992149 at 80iterations 1.1313101E-02 0.3814940 at 90iterations 5.3243465E-03 0.1499519 at 100iterations 2.5290132E-03 7.8417778E-02 at 110iterations 1.1936261E-03 3.3448696E-02 at 120iterations finished qdiffx linear iterations at : 14:36:22 total time elapsed so far: 7.070000 # loops : 120 mean,max change (kT/e) : 1.1936261E-03 3.3448696E-02 energy calculations done at 7.070000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.240000 DelPhi exited at 14:36:22 7.239u 0.183s 0:07.82 94.7% 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 14:36:22 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3009 !!! WARNING: GLU 313 has a net charge of -0.2720 !!! 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.845926 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): -32.10300 24.18800 ymin,ymax (A): -22.98700 23.71700 zmin,zma (A): -11.29700 42.89300 x,y,z range (A): 56.29100 46.70400 54.19000 scale (grids/A): 2.845926 object centre (A): -3.957500 0.3649998 15.79800 number of atom coordinates read : 3009 total number of charged atoms : 2864 net assigned charge : 1.728008 assigned positive charge : 451.0046 centred at (gu) : 97.18586 89.99807 84.84715 assigned negative charge : -449.2773 centred at (gu) : 97.11506 90.68443 84.64331 start vw surface at 0.1600000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 199842 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23897 grid for indexing accessible points = 1.400000 m= 100773 mr = 149777 m= 34728 mr = 83784 m= 7834 mr = 28041 m= 1156 mr = 5807 m= 68 mr = 800 m= 0 mr = 28 time to grow re-entrant surface = 0.8400000 no. cavity mid-points inaccessible to solvent = 602 time to turn everything in is 1.440000 number of dielectric boundary points 76164 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.570000 number of grid points assigned charge 22912 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) : 1.897284 object centre at (A) : -3.957500 0.3649998 15.79800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4035798 0.1427035 midg,1,midg; midg,igrid,midg 0.3126455 -4.1708171E-02 1,midg,midg; igrid,midg,midg 1.4270591E-02 0.1783916 gauss-seidel spectral radius is 0.9992684 estimated iterations to convergence 292 setup time was (sec) 1.730000 now iterating at: 14:36:24 rms-change max change #iterations 10.67101 408.6888 at 10iterations 6.237560 127.7202 at 20iterations 3.614253 64.12181 at 30iterations 2.097667 44.96517 at 40iterations 1.213986 21.77053 at 50iterations 0.6999420 12.60275 at 60iterations 0.4047993 8.623220 at 70iterations 0.2340489 4.085779 at 80iterations 0.1351044 2.216431 at 90iterations 7.7895194E-02 1.334119 at 100iterations 4.4854499E-02 0.7824259 at 110iterations 2.5924783E-02 0.4243851 at 120iterations 1.4953349E-02 0.2442551 at 130iterations 8.6094057E-03 0.1634712 at 140iterations 4.9622608E-03 8.0217361E-02 at 150iterations 2.8611650E-03 5.0445676E-02 at 160iterations 1.6510150E-03 2.9830933E-02 at 170iterations 9.5102895E-04 1.5983582E-02 at 180iterations finished qdiffx linear iterations at : 14:36:34 total time elapsed so far: 11.30000 # loops : 180 mean,max change (kT/e) : 9.5102895E-04 1.5983582E-02 energy calculations done at 11.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.47000 DelPhi exited at 14:36:34 11.469u 0.177s 0:11.94 97.4% 0+0k 0+0io 0pf+0w