Tue Oct 11 03:13:51 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 Tue Oct 11 2011 at 03:13:51 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4130 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: 0.5638979 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): -27.42600 31.00500 ymin,ymax (A): -25.36900 34.93100 zmin,zma (A): -28.58700 34.54500 x,y,z range (A): 58.43100 60.30000 63.13200 scale (grids/A): 0.5638979 object centre (A): 1.789500 4.781000 2.978999 number of atom coordinates read : 4130 total number of charged atoms : 3989 net assigned charge : -3.499954 assigned positive charge : 618.3162 centred at (gu) : 92.28051 90.63042 90.18355 assigned negative charge : -621.8190 centred at (gu) : 92.25299 90.71922 90.18604 start vw surface at 0.1200000 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 8782 nv = 96 ne = 84 npr = 81270 no. pairs analyzed = 81270 no. exposed pairs = 5462 no. arc points = 39216 no. surface atoms = 1824 nbur = 2306 mkacc time = 0.1400000 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= 351 mr = 4426 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.2900000 number of dielectric boundary points 4689 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4016 ## 539 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 11344 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.6804323E-10 -4.9262960E-10 midg,1,midg; midg,igrid,midg 9.6122466E-10 -2.3472122E-09 1,midg,midg; igrid,midg,midg -5.3484395E-10 1.2003547E-10 gauss-seidel spectral radius is 0.9838798 estimated iterations to convergence 65 setup time was (sec) 0.4900000 now iterating at: 03:13:51 rms-change max change #iterations 0.1023681 15.88903 at 10iterations 7.4812253E-03 0.9183283 at 20iterations 6.1188225E-04 8.7726593E-02 at 30iterations 8.4690713E-05 1.4806151E-02 at 40iterations 2.1458529E-05 4.0597916E-03 at 50iterations finished qdiffx linear iterations at : 03:13:54 total time elapsed so far: 3.380000 # loops : 50 mean,max change (kT/e) : 2.1458529E-05 4.0597916E-03 energy calculations done at 3.380000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.520000 DelPhi exited at 03:13:55 3.524u 0.169s 0:04.03 91.3% 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 Tue Oct 11 2011 at 03:13:55 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4130 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: 1.691694 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): -27.42600 31.00500 ymin,ymax (A): -25.36900 34.93100 zmin,zma (A): -28.58700 34.54500 x,y,z range (A): 58.43100 60.30000 63.13200 scale (grids/A): 1.691694 object centre (A): 1.789500 4.781000 2.978999 number of atom coordinates read : 4130 total number of charged atoms : 3989 net assigned charge : -3.499954 assigned positive charge : 618.3162 centred at (gu) : 96.84018 91.88999 90.54900 assigned negative charge : -621.8190 centred at (gu) : 96.75832 92.15714 90.55770 start vw surface at 0.1300000 fill in re-entrant regions at 0.2300000 boundary points on vw surface= 96310 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39216 grid for indexing accessible points = 1.400000 m= 30184 mr = 64102 m= 3369 mr = 20621 m= 100 mr = 1668 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 588 time to turn everything in is 0.4700000 number of dielectric boundary points 43563 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 435 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 30781 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) : 0.5638979 object centre at (A) : 1.789500 4.781000 2.978999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.1926122E-02 -4.4344485E-02 midg,1,midg; midg,igrid,midg 3.8581910E-03 -2.0914836E-02 1,midg,midg; igrid,midg,midg 5.6030080E-03 2.2293724E-02 gauss-seidel spectral radius is 0.9984401 estimated iterations to convergence 201 setup time was (sec) 0.7100000 now iterating at: 03:13:56 rms-change max change #iterations 4.324345 170.7553 at 10iterations 1.905460 57.06149 at 20iterations 0.8466703 24.94597 at 30iterations 0.3755572 11.18663 at 40iterations 0.1666256 4.723611 at 50iterations 7.4248992E-02 2.472252 at 60iterations 3.2951351E-02 1.012540 at 70iterations 1.4646428E-02 0.4515686 at 80iterations 6.5326025E-03 0.1886888 at 90iterations 2.9093968E-03 8.9374542E-02 at 100iterations 1.2908066E-03 3.7673950E-02 at 110iterations 5.7680625E-04 1.8327236E-02 at 120iterations finished qdiffx linear iterations at : 03:14:03 total time elapsed so far: 7.870000 # loops : 120 mean,max change (kT/e) : 5.7680625E-04 1.8327236E-02 energy calculations done at 7.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.010000 DelPhi exited at 03:14:03 8.011u 0.179s 0:08.50 96.2% 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 Tue Oct 11 2011 at 03:14:03 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4130 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: 2.537540 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): -27.42600 31.00500 ymin,ymax (A): -25.36900 34.93100 zmin,zma (A): -28.58700 34.54500 x,y,z range (A): 58.43100 60.30000 63.13200 scale (grids/A): 2.537540 object centre (A): 1.789500 4.781000 2.978999 number of atom coordinates read : 4130 total number of charged atoms : 3989 net assigned charge : -3.499954 assigned positive charge : 618.3162 centred at (gu) : 100.2599 92.83485 90.82333 assigned negative charge : -621.8190 centred at (gu) : 100.1375 93.23540 90.83640 start vw surface at 0.1100000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 223102 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39216 grid for indexing accessible points = 1.400000 m= 103583 mr = 156876 m= 30799 mr = 81396 m= 5413 mr = 22999 m= 422 mr = 3572 m= 6 mr = 192 m= 0 mr = 0 time to grow re-entrant surface = 0.6400000 no. cavity mid-points inaccessible to solvent = 2187 time to turn everything in is 1.130000 number of dielectric boundary points 98290 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 1.230000 number of grid points assigned charge 31883 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) : 1.691694 object centre at (A) : 1.789500 4.781000 2.978999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3724322 -0.9214664 midg,1,midg; midg,igrid,midg 2.4778122E-02 -0.2629913 1,midg,midg; igrid,midg,midg 5.9322987E-02 0.2860631 gauss-seidel spectral radius is 0.9992546 estimated iterations to convergence 289 setup time was (sec) 1.370000 now iterating at: 03:14:05 rms-change max change #iterations 11.10764 321.1512 at 10iterations 6.589076 161.1010 at 20iterations 3.866010 92.29924 at 30iterations 2.263267 41.90815 at 40iterations 1.319059 29.02817 at 50iterations 0.7652461 18.24204 at 60iterations 0.4427305 7.503792 at 70iterations 0.2559021 4.481380 at 80iterations 0.1478088 2.543161 at 90iterations 8.5118964E-02 1.565975 at 100iterations 4.9030781E-02 0.8653831 at 110iterations 2.8185030E-02 0.4899979 at 120iterations 1.6198013E-02 0.2793913 at 130iterations 9.3370723E-03 0.1672931 at 140iterations 5.3631025E-03 9.2212677E-02 at 150iterations 3.0866445E-03 4.9606323E-02 at 160iterations 1.7757375E-03 3.1498909E-02 at 170iterations 1.0221832E-03 1.8079758E-02 at 180iterations finished qdiffx linear iterations at : 03:14:17 total time elapsed so far: 13.10000 # loops : 180 mean,max change (kT/e) : 1.0221832E-03 1.8079758E-02 energy calculations done at 13.10000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.23000 DelPhi exited at 03:14:17 13.233u 0.211s 0:13.76 97.6% 0+0k 0+0io 0pf+0w