Sun Oct 9 17:35:53 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 17:35:53 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5018 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 0.5639515 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): 3.241000 65.01000 ymin,ymax (A): -8.630000 53.52700 zmin,zma (A): -1.208000 61.91800 x,y,z range (A): 61.76900 62.15700 63.12600 scale (grids/A): 0.5639515 object centre (A): 34.12550 22.44850 30.35500 number of atom coordinates read : 5018 total number of charged atoms : 4875 net assigned charge : 0.1350489 assigned positive charge : 773.7959 centred at (gu) : 88.36148 89.25170 89.17116 assigned negative charge : -773.6666 centred at (gu) : 88.25769 89.28764 89.14092 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 10478 nv = 96 ne = 84 npr = 101358 no. pairs analyzed = 101358 no. exposed pairs = 5943 no. arc points = 40182 no. surface atoms = 2018 nbur = 3000 mkacc time = 0.2400000 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 = 1.540000 m= 482 mr = 6023 m= 3 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 4919 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4072 ## 435 charges are in solution ## iepsmp to db, and charging done at 0.6300000 number of grid points assigned charge 13647 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -7.4848283E-10 5.9177369E-10 midg,1,midg; midg,igrid,midg 1.0197714E-09 -6.1438526E-10 1,midg,midg; igrid,midg,midg -3.3893044E-09 1.5610239E-09 gauss-seidel spectral radius is 0.9839312 estimated iterations to convergence 65 setup time was (sec) 0.7500000 now iterating at: 17:35:54 rms-change max change #iterations 0.1193072 17.18480 at 10iterations 1.0910012E-02 1.491440 at 20iterations 3.0722797E-03 0.3523407 at 30iterations 1.4635110E-03 0.1668938 at 40iterations 7.2847068E-04 8.7706894E-02 at 50iterations finished qdiffx linear iterations at : 17:35:57 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 7.2847068E-04 8.7706894E-02 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 17:35:57 3.543u 0.138s 0:04.01 91.5% 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 17:35:57 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5018 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.691854 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): 3.241000 65.01000 ymin,ymax (A): -8.630000 53.52700 zmin,zma (A): -1.208000 61.91800 x,y,z range (A): 61.76900 62.15700 63.12600 scale (grids/A): 1.691854 object centre (A): 34.12550 22.44850 30.35500 number of atom coordinates read : 5018 total number of charged atoms : 4875 net assigned charge : 0.1350489 assigned positive charge : 773.7959 centred at (gu) : 85.08292 87.75355 87.51194 assigned negative charge : -773.6666 centred at (gu) : 84.77290 87.86287 87.42281 start vw surface at 0.2100000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 117001 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40182 grid for indexing accessible points = 1.400000 m= 41354 mr = 84960 m= 5347 mr = 30036 m= 191 mr = 2987 m= 0 mr = 40 time to grow re-entrant surface = 0.4200000 no. cavity mid-points inaccessible to solvent = 58 time to turn everything in is 0.8300000 number of dielectric boundary points 45870 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 359 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 37604 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) : 0.5639515 object centre at (A) : 34.12550 22.44850 30.35500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.0892000E-02 -2.8413121E-02 midg,1,midg; midg,igrid,midg 1.7796369E-02 8.2159145E-03 1,midg,midg; igrid,midg,midg -1.9810516E-02 2.8291343E-02 gauss-seidel spectral radius is 0.9984991 estimated iterations to convergence 205 setup time was (sec) 1.130000 now iterating at: 17:35:58 rms-change max change #iterations 5.031310 255.1514 at 10iterations 2.261244 63.70868 at 20iterations 1.023600 28.50541 at 30iterations 0.4645213 12.91157 at 40iterations 0.2099726 5.909678 at 50iterations 9.5360152E-02 2.518383 at 60iterations 4.3645371E-02 1.155910 at 70iterations 2.0244433E-02 0.5560765 at 80iterations 9.8373713E-03 0.2872887 at 90iterations 5.2523320E-03 0.1461716 at 100iterations 3.2015694E-03 8.1756592E-02 at 110iterations 2.2220365E-03 5.5495262E-02 at 120iterations finished qdiffx linear iterations at : 17:36:05 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 2.2220365E-03 5.5495262E-02 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.900000 DelPhi exited at 17:36:05 7.900u 0.167s 0:08.33 96.7% 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 Sun Oct 9 2011 at 17:36:06 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: 298 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5018 !!! WARNING: HIQ 377 has a net charge of 0.5140 !!! WARNING: PLP 999 has a net charge of -0.3790 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: 2.537782 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): 3.241000 65.01000 ymin,ymax (A): -8.630000 53.52700 zmin,zma (A): -1.208000 61.91800 x,y,z range (A): 61.76900 62.15700 63.12600 scale (grids/A): 2.537782 object centre (A): 34.12550 22.44850 30.35500 number of atom coordinates read : 5018 total number of charged atoms : 4875 net assigned charge : 0.1350489 assigned positive charge : 773.7959 centred at (gu) : 82.62400 86.63005 86.26734 assigned negative charge : -773.6666 centred at (gu) : 82.15938 86.79423 86.13417 start vw surface at 0.2200000 fill in re-entrant regions at 0.6700000 boundary points on vw surface= 271887 reading accessible surface arcs data from file ARCDAT no. of arc points read = 40182 grid for indexing accessible points = 1.400000 m= 138597 mr = 206656 m= 45181 mr = 113155 m= 8888 mr = 35257 m= 817 mr = 6173 m= 17 mr = 459 m= 0 mr = 0 time to grow re-entrant surface = 1.290000 no. cavity mid-points inaccessible to solvent = 154 time to turn everything in is 2.100000 number of dielectric boundary points 103687 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 13 iepsmp to db, and charging done at 2.230000 number of grid points assigned charge 38980 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) : 1.691854 object centre at (A) : 34.12550 22.44850 30.35500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4720715 -0.6666314 midg,1,midg; midg,igrid,midg -6.6702832E-03 -9.6414033E-03 1,midg,midg; igrid,midg,midg -0.4014986 0.3201144 gauss-seidel spectral radius is 0.9992720 estimated iterations to convergence 292 setup time was (sec) 2.400000 now iterating at: 17:36:08 rms-change max change #iterations 12.59725 493.3331 at 10iterations 7.470248 231.3721 at 20iterations 4.414541 103.2117 at 30iterations 2.599433 49.18454 at 40iterations 1.520805 27.10315 at 50iterations 0.8879057 16.45040 at 60iterations 0.5177880 8.117111 at 70iterations 0.3018502 4.588308 at 80iterations 0.1754227 2.680359 at 90iterations 0.1019427 1.614502 at 100iterations 5.9211571E-02 0.9464188 at 110iterations 3.4582715E-02 0.5582047 at 120iterations 2.0317946E-02 0.3381348 at 130iterations 1.2066387E-02 0.2091675 at 140iterations 7.3797619E-03 0.1289711 at 150iterations 4.7351080E-03 8.4686279E-02 at 160iterations 3.2439437E-03 5.3661346E-02 at 170iterations 2.4038595E-03 4.1248322E-02 at 180iterations finished qdiffx linear iterations at : 17:36:19 total time elapsed so far: 12.96000 # loops : 180 mean,max change (kT/e) : 2.4038595E-03 4.1248322E-02 energy calculations done at 12.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.15000 DelPhi exited at 17:36:19 13.151u 0.195s 0:13.64 97.8% 0+0k 0+0io 0pf+0w