Sun Oct 9 19:06:22 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 19:06:23 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5290 !!! 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: 0.5471704 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): 3.229000 68.29100 ymin,ymax (A): -8.874000 52.19800 zmin,zma (A): -1.029000 63.54400 x,y,z range (A): 65.06200 61.07200 64.57301 scale (grids/A): 0.5471704 object centre (A): 35.76000 21.66200 31.25750 number of atom coordinates read : 5290 total number of charged atoms : 5144 net assigned charge : 0.6210479 assigned positive charge : 813.8619 centred at (gu) : 88.14300 89.53364 89.15205 assigned negative charge : -813.2475 centred at (gu) : 88.01425 89.57748 89.08195 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 10364 nv = 96 ne = 84 npr = 106781 no. pairs analyzed = 106781 no. exposed pairs = 6092 no. arc points = 41779 no. surface atoms = 2089 nbur = 3201 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 = 1.568000 m= 446 mr = 5958 m= 0 mr = 23 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4800000 number of dielectric boundary points 4829 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4183 ## 463 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 13551 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0070000E-09 7.7600915E-10 midg,1,midg; midg,igrid,midg 7.1047074E-10 -4.2328038E-10 1,midg,midg; igrid,midg,midg -2.5231430E-09 1.0608651E-09 gauss-seidel spectral radius is 0.9829457 estimated iterations to convergence 63 setup time was (sec) 0.7400000 now iterating at: 19:06:23 rms-change max change #iterations 0.1038056 14.47715 at 10iterations 1.0327144E-02 1.584709 at 20iterations 3.4704776E-03 0.4323349 at 30iterations 1.6388575E-03 0.2006950 at 40iterations 7.9613976E-04 0.1021852 at 50iterations finished qdiffx linear iterations at : 19:06:26 total time elapsed so far: 3.500000 # loops : 50 mean,max change (kT/e) : 7.9613976E-04 0.1021852 energy calculations done at 3.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.660000 DelPhi exited at 19:06:27 3.668u 0.232s 0:04.20 92.6% 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 Sun Oct 9 2011 at 19:06:27 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5290 !!! 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: 1.641511 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): 3.229000 68.29100 ymin,ymax (A): -8.874000 52.19800 zmin,zma (A): -1.029000 63.54400 x,y,z range (A): 65.06200 61.07200 64.57301 scale (grids/A): 1.641511 object centre (A): 35.76000 21.66200 31.25750 number of atom coordinates read : 5290 total number of charged atoms : 5144 net assigned charge : 0.6210479 assigned positive charge : 813.8619 centred at (gu) : 84.42786 88.59975 87.45475 assigned negative charge : -813.2475 centred at (gu) : 84.04282 88.73218 87.24567 start vw surface at 0.2100000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 116098 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41779 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 39933 mr = 84445 m= 4691 mr = 29121 m= 128 mr = 2510 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 46 time to turn everything in is 0.7900000 number of dielectric boundary points 44756 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 425 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 39416 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) : 0.5471704 object centre at (A) : 35.76000 21.66200 31.25750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.8188007E-02 7.0124748E-03 midg,1,midg; midg,igrid,midg 2.0014631E-02 7.4524772E-03 1,midg,midg; igrid,midg,midg -2.6405392E-02 7.2535244E-03 gauss-seidel spectral radius is 0.9984134 estimated iterations to convergence 199 setup time was (sec) 1.100000 now iterating at: 19:06:28 rms-change max change #iterations 4.836036 213.3449 at 10iterations 2.132375 65.64607 at 20iterations 0.9422926 24.40266 at 30iterations 0.4173556 13.38711 at 40iterations 0.1853446 5.106309 at 50iterations 8.2353905E-02 2.293901 at 60iterations 3.7206374E-02 1.012512 at 70iterations 1.7174160E-02 0.4929199 at 80iterations 8.5081216E-03 0.2497418 at 90iterations 4.7704587E-03 0.1320114 at 100iterations 3.0630543E-03 8.4928513E-02 at 110iterations 2.1790487E-03 5.7759285E-02 at 120iterations finished qdiffx linear iterations at : 19:06:35 total time elapsed so far: 8.300000 # loops : 120 mean,max change (kT/e) : 2.1790487E-03 5.7759285E-02 energy calculations done at 8.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.460000 DelPhi exited at 19:06:36 8.460u 0.296s 0:09.07 96.4% 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 19:06:36 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: 252 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 5290 !!! 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 2.462267 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): 3.229000 68.29100 ymin,ymax (A): -8.874000 52.19800 zmin,zma (A): -1.029000 63.54400 x,y,z range (A): 65.06200 61.07200 64.57301 scale (grids/A): 2.462267 object centre (A): 35.76000 21.66200 31.25750 number of atom coordinates read : 5290 total number of charged atoms : 5144 net assigned charge : 0.6210479 assigned positive charge : 813.8619 centred at (gu) : 81.64140 87.89910 86.18172 assigned negative charge : -813.2475 centred at (gu) : 81.06418 88.09833 85.86845 start vw surface at 0.1800000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 269696 reading accessible surface arcs data from file ARCDAT no. of arc points read = 41779 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 136060 mr = 205260 m= 42430 mr = 111637 m= 7465 mr = 32927 m= 581 mr = 5129 m= 14 mr = 278 m= 0 mr = 0 time to grow re-entrant surface = 1.200000 no. cavity mid-points inaccessible to solvent = 159 time to turn everything in is 1.940000 number of dielectric boundary points 101015 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 2.100000 number of grid points assigned charge 41106 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) : 1.641511 object centre at (A) : 35.76000 21.66200 31.25750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.4390078 0.1079145 midg,1,midg; midg,igrid,midg 0.2138587 -2.3309276E-02 1,midg,midg; igrid,midg,midg -0.4925950 0.1271349 gauss-seidel spectral radius is 0.9992502 estimated iterations to convergence 288 setup time was (sec) 2.300000 now iterating at: 19:06:38 rms-change max change #iterations 12.27135 340.1425 at 10iterations 7.211586 158.1892 at 20iterations 4.214265 86.37968 at 30iterations 2.449453 42.45993 at 40iterations 1.422297 25.78727 at 50iterations 0.8222465 14.48774 at 60iterations 0.4751302 7.700583 at 70iterations 0.2736118 4.395027 at 80iterations 0.1577415 2.483080 at 90iterations 9.0898491E-02 1.346649 at 100iterations 5.2415065E-02 0.7934647 at 110iterations 3.0265011E-02 0.4835569 at 120iterations 1.7595446E-02 0.3032475 at 130iterations 1.0400194E-02 0.1783829 at 140iterations 6.3131237E-03 0.1136475 at 150iterations 4.0053139E-03 7.6271057E-02 at 160iterations 2.7238228E-03 4.9201965E-02 at 170iterations 1.9914869E-03 3.5278320E-02 at 180iterations finished qdiffx linear iterations at : 19:06:50 total time elapsed so far: 13.89000 # loops : 180 mean,max change (kT/e) : 1.9914869E-03 3.5278320E-02 energy calculations done at 13.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.06000 DelPhi exited at 19:06:51 14.064u 0.299s 0:14.65 97.9% 0+0k 0+0io 0pf+0w