Mon Oct 10 14:37:32 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 Mon Oct 10 2011 at 14:37:32 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 = 3103 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5256552 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): -9.534000 47.42100 ymin,ymax (A): -16.75300 35.52200 zmin,zma (A): -24.88800 42.83700 x,y,z range (A): 56.95500 52.27500 67.72501 scale (grids/A): 0.5256552 object centre (A): 18.94350 9.384500 8.974501 number of atom coordinates read : 3103 total number of charged atoms : 2967 net assigned charge : 1.500009 assigned positive charge : 471.2199 centred at (gu) : 88.60078 88.07183 90.55303 assigned negative charge : -469.7211 centred at (gu) : 88.49079 88.11485 90.42875 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5590 nv = 96 ne = 84 npr = 60904 no. pairs analyzed = 60904 no. exposed pairs = 4272 no. arc points = 29644 no. surface atoms = 1431 nbur = 1672 mkacc time = 9.9999994E-02 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 = 1.624000 m= 254 mr = 2704 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3130 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2940 ## 404 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 7361 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.1026964E-10 4.9435644E-10 midg,1,midg; midg,igrid,midg 2.9197134E-10 -5.7676648E-11 1,midg,midg; igrid,midg,midg -4.5160711E-10 2.6815178E-10 gauss-seidel spectral radius is 0.9813739 estimated iterations to convergence 60 setup time was (sec) 0.4200000 now iterating at: 14:37:32 rms-change max change #iterations 6.1922364E-02 11.01488 at 10iterations 4.2250757E-03 0.7381001 at 20iterations 4.6457190E-04 8.8478088E-02 at 30iterations 8.8912893E-05 1.6868591E-02 at 40iterations 1.9073863E-05 3.5858154E-03 at 50iterations finished qdiffx linear iterations at : 14:37:35 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 1.9073863E-05 3.5858154E-03 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 14:37:36 3.441u 0.174s 0:04.11 87.8% 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 Mon Oct 10 2011 at 14:37:36 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3103 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.576966 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): -9.534000 47.42100 ymin,ymax (A): -16.75300 35.52200 zmin,zma (A): -24.88800 42.83700 x,y,z range (A): 56.95500 52.27500 67.72501 scale (grids/A): 1.576966 object centre (A): 18.94350 9.384500 8.974501 number of atom coordinates read : 3103 total number of charged atoms : 2967 net assigned charge : 1.500009 assigned positive charge : 471.2199 centred at (gu) : 85.80175 84.21442 91.65829 assigned negative charge : -469.7211 centred at (gu) : 85.47195 84.34405 91.28578 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 61958 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29644 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 18806 mr = 40312 m= 2033 mr = 12254 m= 61 mr = 919 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 29373 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 326 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 22437 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) : 0.5256552 object centre at (A) : 18.94350 9.384500 8.974501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.5339552E-03 2.7581159E-02 midg,1,midg; midg,igrid,midg 2.3260086E-03 -7.0367586E-03 1,midg,midg; igrid,midg,midg -1.0480628E-02 1.0816953E-03 gauss-seidel spectral radius is 0.9980675 estimated iterations to convergence 181 setup time was (sec) 0.5300000 now iterating at: 14:37:37 rms-change max change #iterations 3.145787 168.8482 at 10iterations 1.274497 58.46616 at 20iterations 0.5149947 19.90061 at 30iterations 0.2081929 9.124889 at 40iterations 8.4749170E-02 3.084504 at 50iterations 3.4535266E-02 1.276984 at 60iterations 1.4047107E-02 0.4839211 at 70iterations 5.7361745E-03 0.2127781 at 80iterations 2.3671295E-03 8.7873459E-02 at 90iterations 9.9244702E-04 4.5112610E-02 at 100iterations 4.2762214E-04 1.6506195E-02 at 110iterations 1.9143699E-04 7.2135925E-03 at 120iterations finished qdiffx linear iterations at : 14:37:44 total time elapsed so far: 7.650000 # loops : 120 mean,max change (kT/e) : 1.9143699E-04 7.2135925E-03 energy calculations done at 7.650000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.780000 DelPhi exited at 14:37:44 7.781u 0.212s 0:08.32 96.0% 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 Mon Oct 10 2011 at 14:37:44 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 = 3103 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.365448 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): -9.534000 47.42100 ymin,ymax (A): -16.75300 35.52200 zmin,zma (A): -24.88800 42.83700 x,y,z range (A): 56.95500 52.27500 67.72501 scale (grids/A): 2.365448 object centre (A): 18.94350 9.384500 8.974501 number of atom coordinates read : 3103 total number of charged atoms : 2967 net assigned charge : 1.500009 assigned positive charge : 471.2199 centred at (gu) : 83.70238 81.32148 92.48724 assigned negative charge : -469.7211 centred at (gu) : 83.20787 81.51601 91.92857 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 144016 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29644 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 64816 mr = 99654 m= 18767 mr = 49644 m= 3025 mr = 13264 m= 188 mr = 1840 m= 5 mr = 59 m= 0 mr = 0 time to grow re-entrant surface = 0.4300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7600000 number of dielectric boundary points 66356 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 33 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 23685 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) : 1.576966 object centre at (A) : 18.94350 9.384500 8.974501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3318830E-02 0.4900963 midg,1,midg; midg,igrid,midg 5.0750468E-02 -0.1298314 1,midg,midg; igrid,midg,midg -0.1642563 4.5256466E-03 gauss-seidel spectral radius is 0.9991017 estimated iterations to convergence 264 setup time was (sec) 0.9900000 now iterating at: 14:37:45 rms-change max change #iterations 8.506938 362.8552 at 10iterations 4.773555 144.2556 at 20iterations 2.661204 65.14800 at 30iterations 1.474250 42.88301 at 40iterations 0.8106657 19.02576 at 50iterations 0.4450263 10.14973 at 60iterations 0.2431104 5.829134 at 70iterations 0.1327199 3.269426 at 80iterations 7.2560355E-02 1.513890 at 90iterations 3.9467782E-02 0.9018879 at 100iterations 2.1471091E-02 0.4737682 at 110iterations 1.1713495E-02 0.2724628 at 120iterations 6.3675856E-03 0.1464882 at 130iterations 3.4621961E-03 9.7488165E-02 at 140iterations 1.8848812E-03 4.1898727E-02 at 150iterations 1.0273387E-03 2.2678375E-02 at 160iterations 5.6299660E-04 1.1425972E-02 at 170iterations 3.0986933E-04 7.1086884E-03 at 180iterations finished qdiffx linear iterations at : 14:37:57 total time elapsed so far: 12.17000 # loops : 180 mean,max change (kT/e) : 3.0986933E-04 7.1086884E-03 energy calculations done at 12.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.30000 DelPhi exited at 14:37:57 12.300u 0.218s 0:13.05 95.8% 0+0k 0+0io 0pf+0w