Sun Oct 9 22:35:22 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 Sun Oct 9 2011 at 22:35:22 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3572 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5522719 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): -25.04400 28.48300 ymin,ymax (A): -31.52000 24.84100 zmin,zma (A): -78.97100 -14.51000 x,y,z range (A): 53.52700 56.36100 64.46100 scale (grids/A): 0.5522719 object centre (A): 1.719501 -3.339500 -46.74050 number of atom coordinates read : 3572 total number of charged atoms : 3422 net assigned charge : 8.000015 assigned positive charge : 547.4683 centred at (gu) : 89.55837 89.45243 89.79267 assigned negative charge : -539.4706 centred at (gu) : 89.62190 89.47545 89.70300 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7161 nv = 96 ne = 84 npr = 67918 no. pairs analyzed = 67918 no. exposed pairs = 4770 no. arc points = 35401 no. surface atoms = 1587 nbur = 1985 mkacc time = 0.1500000 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= 298 mr = 3405 m= 1 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.3500000 number of dielectric boundary points 4049 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3599 ## 499 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9401 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.0657768E-10 1.4604770E-09 midg,1,midg; midg,igrid,midg 9.8980280E-10 3.5147160E-10 1,midg,midg; igrid,midg,midg 1.4203427E-09 -1.3420902E-11 gauss-seidel spectral radius is 0.9831554 estimated iterations to convergence 63 setup time was (sec) 0.5700000 now iterating at: 22:35:23 rms-change max change #iterations 8.7237358E-02 13.55961 at 10iterations 5.8899070E-03 1.077612 at 20iterations 4.0456312E-04 6.1558723E-02 at 30iterations 2.8018974E-05 4.4016838E-03 at 40iterations 2.1857102E-06 3.2711029E-04 at 50iterations finished qdiffx linear iterations at : 22:35:25 total time elapsed so far: 3.060000 # loops : 50 mean,max change (kT/e) : 2.1857102E-06 3.2711029E-04 energy calculations done at 3.060000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.240000 DelPhi exited at 22:35:26 3.241u 0.139s 0:03.73 90.3% 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 Sun Oct 9 2011 at 22:35:26 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 = 3572 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: 1.656816 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): -25.04400 28.48300 ymin,ymax (A): -31.52000 24.84100 zmin,zma (A): -78.97100 -14.51000 x,y,z range (A): 53.52700 56.36100 64.46100 scale (grids/A): 1.656816 object centre (A): 1.719501 -3.339500 -46.74050 number of atom coordinates read : 3572 total number of charged atoms : 3422 net assigned charge : 8.000015 assigned positive charge : 547.4683 centred at (gu) : 88.67361 88.35619 89.37706 assigned negative charge : -539.4706 centred at (gu) : 88.86532 88.42596 89.10843 start vw surface at 0.2100000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 79237 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35401 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 22542 mr = 50868 m= 2360 mr = 14617 m= 78 mr = 1113 m= 0 mr = 6 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 2376 time to turn everything in is 0.5700000 number of dielectric boundary points 37613 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 404 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 26281 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) : 0.5522719 object centre at (A) : 1.719501 -3.339500 -46.74050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.1906931E-03 1.8491058E-02 midg,1,midg; midg,igrid,midg 8.8493777E-03 -4.1016098E-03 1,midg,midg; igrid,midg,midg 1.7182281E-02 1.0257950E-02 gauss-seidel spectral radius is 0.9983332 estimated iterations to convergence 194 setup time was (sec) 0.8400000 now iterating at: 22:35:27 rms-change max change #iterations 3.819501 164.2437 at 10iterations 1.640668 62.05157 at 20iterations 0.7063023 24.32515 at 30iterations 0.3033813 10.21071 at 40iterations 0.1309817 4.416893 at 50iterations 5.6474209E-02 1.858273 at 60iterations 2.4375033E-02 0.8134079 at 70iterations 1.0510573E-02 0.3923736 at 80iterations 4.5320690E-03 0.1551452 at 90iterations 1.9650068E-03 6.5798759E-02 at 100iterations 8.4786466E-04 2.9026031E-02 at 110iterations 3.6687742E-04 1.2832642E-02 at 120iterations finished qdiffx linear iterations at : 22:35:33 total time elapsed so far: 7.220000 # loops : 120 mean,max change (kT/e) : 3.6687742E-04 1.2832642E-02 energy calculations done at 7.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.400000 DelPhi exited at 22:35:34 7.406u 0.159s 0:07.93 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 22:35:34 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 = 3572 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.485224 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): -25.04400 28.48300 ymin,ymax (A): -31.52000 24.84100 zmin,zma (A): -78.97100 -14.51000 x,y,z range (A): 53.52700 56.36100 64.46100 scale (grids/A): 2.485224 object centre (A): 1.719501 -3.339500 -46.74050 number of atom coordinates read : 3572 total number of charged atoms : 3422 net assigned charge : 8.000015 assigned positive charge : 547.4683 centred at (gu) : 88.01021 87.53398 89.06533 assigned negative charge : -539.4706 centred at (gu) : 88.29796 87.63897 88.66251 start vw surface at 0.2100000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 184026 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35401 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 79143 mr = 125403 m= 21598 mr = 60537 m= 3733 mr = 15506 m= 301 mr = 2330 m= 2 mr = 132 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 7823 time to turn everything in is 1.280000 number of dielectric boundary points 84895 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 22 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 27349 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) : 1.656816 object centre at (A) : 1.719501 -3.339500 -46.74050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.8093942E-02 0.2926016 midg,1,midg; midg,igrid,midg 0.1547462 -9.3419679E-02 1,midg,midg; igrid,midg,midg 0.2767677 0.1561095 gauss-seidel spectral radius is 0.9992099 estimated iterations to convergence 281 setup time was (sec) 1.560000 now iterating at: 22:35:35 rms-change max change #iterations 9.865421 367.2307 at 10iterations 5.754826 144.9160 at 20iterations 3.318908 83.66470 at 30iterations 1.899126 37.14217 at 40iterations 1.085381 23.57938 at 50iterations 0.6179337 12.90222 at 60iterations 0.3512386 7.130267 at 70iterations 0.1991920 3.991318 at 80iterations 0.1128336 2.087070 at 90iterations 6.3930668E-02 1.366446 at 100iterations 3.6158212E-02 0.6584988 at 110iterations 2.0435438E-02 0.3736038 at 120iterations 1.1515066E-02 0.2024784 at 130iterations 6.5127886E-03 0.1225586 at 140iterations 3.6735972E-03 6.8780899E-02 at 150iterations 2.0754181E-03 3.7909508E-02 at 160iterations 1.1683336E-03 2.2624969E-02 at 170iterations 6.6021131E-04 1.1725903E-02 at 180iterations finished qdiffx linear iterations at : 22:35:45 total time elapsed so far: 11.24000 # loops : 180 mean,max change (kT/e) : 6.6021131E-04 1.1725903E-02 energy calculations done at 11.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.41000 DelPhi exited at 22:35:46 11.417u 0.197s 0:11.92 97.3% 0+0k 0+0io 0pf+0w