Sun Oct 9 07:20:46 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 07:20:46 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2498 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: 0.5440846 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): -5.007000 42.17200 ymin,ymax (A): 35.84800 87.34200 zmin,zma (A): -3.275000 62.15600 x,y,z range (A): 47.17900 51.49400 65.43100 scale (grids/A): 0.5440846 object centre (A): 18.58250 61.59500 29.44050 number of atom coordinates read : 2498 total number of charged atoms : 2353 net assigned charge : -8.499982 assigned positive charge : 373.4329 centred at (gu) : 90.70359 89.07393 89.38152 assigned negative charge : -381.9334 centred at (gu) : 90.86268 88.70636 89.27702 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 4898 nv = 96 ne = 84 npr = 49702 no. pairs analyzed = 49702 no. exposed pairs = 3484 no. arc points = 25097 no. surface atoms = 1170 nbur = 1328 mkacc time = 0.1100000 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 = 1.568000 m= 192 mr = 2288 m= 2 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2700000 number of dielectric boundary points 2798 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2505 ## 331 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 6362 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1843709E-09 7.5780694E-11 midg,1,midg; midg,igrid,midg -3.1534979E-09 1.1108408E-09 1,midg,midg; igrid,midg,midg 3.0833977E-10 -1.5675081E-09 gauss-seidel spectral radius is 0.9825560 estimated iterations to convergence 62 setup time was (sec) 0.5100000 now iterating at: 07:20:47 rms-change max change #iterations 6.3743934E-02 11.16568 at 10iterations 4.0529603E-03 0.7648697 at 20iterations 2.6732677E-04 4.9886703E-02 at 30iterations 1.8957513E-05 3.2577515E-03 at 40iterations 1.7653739E-06 2.7656555E-04 at 50iterations finished qdiffx linear iterations at : 07:20:50 total time elapsed so far: 3.440000 # loops : 50 mean,max change (kT/e) : 1.7653739E-06 2.7656555E-04 energy calculations done at 3.440000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.610000 DelPhi exited at 07:20:51 3.613u 0.250s 0:04.17 92.5% 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 07:20:51 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2498 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: 1.632254 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): -5.007000 42.17200 ymin,ymax (A): 35.84800 87.34200 zmin,zma (A): -3.275000 62.15600 x,y,z range (A): 47.17900 51.49400 65.43100 scale (grids/A): 1.632254 object centre (A): 18.58250 61.59500 29.44050 number of atom coordinates read : 2498 total number of charged atoms : 2353 net assigned charge : -8.499982 assigned positive charge : 373.4329 centred at (gu) : 92.11028 87.22111 88.14408 assigned negative charge : -381.9334 centred at (gu) : 92.58755 86.11878 87.83067 start vw surface at 0.1400000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 53666 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25097 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 15695 mr = 33945 m= 1454 mr = 10364 m= 39 mr = 626 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 141 time to turn everything in is 0.4100000 number of dielectric boundary points 25919 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 308 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 18053 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) : 0.5440846 object centre at (A) : 18.58250 61.59500 29.44050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.4303214E-02 3.8917926E-03 midg,1,midg; midg,igrid,midg -2.1509804E-02 7.8341812E-03 1,midg,midg; igrid,midg,midg -2.2192744E-03 -1.4136079E-02 gauss-seidel spectral radius is 0.9981343 estimated iterations to convergence 184 setup time was (sec) 0.7300000 now iterating at: 07:20:52 rms-change max change #iterations 3.026063 147.0369 at 10iterations 1.242873 61.92347 at 20iterations 0.5092914 21.09521 at 30iterations 0.2092416 8.626265 at 40iterations 8.5961618E-02 3.236089 at 50iterations 3.5369482E-02 1.337922 at 60iterations 1.4534398E-02 0.6037674 at 70iterations 5.9538553E-03 0.2479458 at 80iterations 2.4602653E-03 0.1028957 at 90iterations 1.0143660E-03 4.4726372E-02 at 100iterations 4.1767111E-04 1.7709732E-02 at 110iterations 1.7167575E-04 7.0896149E-03 at 120iterations finished qdiffx linear iterations at : 07:20:59 total time elapsed so far: 7.770000 # loops : 120 mean,max change (kT/e) : 1.7167575E-04 7.0896149E-03 energy calculations done at 7.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 07:20:59 7.945u 0.363s 0:08.71 95.2% 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 Sun Oct 9 2011 at 07:20:59 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2498 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: 2.448381 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): -5.007000 42.17200 ymin,ymax (A): 35.84800 87.34200 zmin,zma (A): -3.275000 62.15600 x,y,z range (A): 47.17900 51.49400 65.43100 scale (grids/A): 2.448381 object centre (A): 18.58250 61.59500 29.44050 number of atom coordinates read : 2498 total number of charged atoms : 2353 net assigned charge : -8.499982 assigned positive charge : 373.4329 centred at (gu) : 93.16518 85.83154 87.21593 assigned negative charge : -381.9334 centred at (gu) : 93.88119 84.17805 86.74586 start vw surface at 0.1600000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 124599 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25097 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 55289 mr = 83810 m= 14581 mr = 42582 m= 2025 mr = 10465 m= 144 mr = 1207 m= 2 mr = 64 m= 0 mr = 0 time to grow re-entrant surface = 0.5100000 no. cavity mid-points inaccessible to solvent = 474 time to turn everything in is 0.9500000 number of dielectric boundary points 58512 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 20 iepsmp to db, and charging done at 1.090000 number of grid points assigned charge 18809 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) : 1.632254 object centre at (A) : 18.58250 61.59500 29.44050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.8746467 4.3743405E-02 midg,1,midg; midg,igrid,midg -0.2884887 0.1076866 1,midg,midg; igrid,midg,midg -3.3157818E-02 -0.1837325 gauss-seidel spectral radius is 0.9991164 estimated iterations to convergence 266 setup time was (sec) 1.270000 now iterating at: 07:21:01 rms-change max change #iterations 7.928669 260.9491 at 10iterations 4.406847 126.3006 at 20iterations 2.459933 64.05057 at 30iterations 1.358285 44.43396 at 40iterations 0.7526327 19.02988 at 50iterations 0.4141538 9.301759 at 60iterations 0.2272823 5.143462 at 70iterations 0.1247307 3.166473 at 80iterations 6.8261899E-02 1.516388 at 90iterations 3.7417013E-02 0.8611040 at 100iterations 2.0488229E-02 0.4765606 at 110iterations 1.1170813E-02 0.2735023 at 120iterations 6.0969582E-03 0.1359501 at 130iterations 3.3373793E-03 7.5073242E-02 at 140iterations 1.8198162E-03 4.5700073E-02 at 150iterations 9.9349860E-04 2.4186134E-02 at 160iterations 5.4212380E-04 1.3336182E-02 at 170iterations 2.9490591E-04 6.6528320E-03 at 180iterations finished qdiffx linear iterations at : 07:21:12 total time elapsed so far: 12.76000 # loops : 180 mean,max change (kT/e) : 2.9490591E-04 6.6528320E-03 energy calculations done at 12.76000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.93000 DelPhi exited at 07:21:13 12.936u 0.285s 0:13.73 96.2% 0+0k 0+0io 0pf+0w