Mon Oct 10 13:59:26 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 13:59:26 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3374 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5994174 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): -2.207000 57.18400 ymin,ymax (A): -23.58300 29.19700 zmin,zma (A): -9.685000 44.84200 x,y,z range (A): 59.39100 52.78000 54.52700 scale (grids/A): 0.5994174 object centre (A): 27.48850 2.807000 17.57850 number of atom coordinates read : 3374 total number of charged atoms : 3227 net assigned charge : 5.500022 assigned positive charge : 506.0926 centred at (gu) : 91.95420 88.64881 90.17350 assigned negative charge : -500.5941 centred at (gu) : 91.97233 88.63065 90.20087 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 7893 nv = 96 ne = 84 npr = 70266 no. pairs analyzed = 70266 no. exposed pairs = 3833 no. arc points = 26822 no. surface atoms = 1303 nbur = 2071 mkacc time = 0.2000000 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 = 1.456000 m= 339 mr = 4472 m= 1 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 3 time to turn everything in is 0.4300000 number of dielectric boundary points 3741 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2736 ## 268 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 9999 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4469589E-09 1.1084045E-09 midg,1,midg; midg,igrid,midg 1.9979987E-09 2.3459876E-09 1,midg,midg; igrid,midg,midg 2.0552418E-09 2.2804549E-09 gauss-seidel spectral radius is 0.9856532 estimated iterations to convergence 68 setup time was (sec) 0.6900000 now iterating at: 13:59:27 rms-change max change #iterations 0.1243512 16.25599 at 10iterations 1.0948484E-02 1.464286 at 20iterations 1.0423037E-03 0.1504297 at 30iterations 1.3370215E-04 1.8474579E-02 at 40iterations 2.7466878E-05 3.5581589E-03 at 50iterations finished qdiffx linear iterations at : 13:59:31 total time elapsed so far: 3.970000 # loops : 50 mean,max change (kT/e) : 2.7466878E-05 3.5581589E-03 energy calculations done at 3.970000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.150000 DelPhi exited at 13:59:31 4.156u 0.267s 0:05.14 85.7% 0+0k 0+0io 5pf+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 13:59:32 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3374 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.798252 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): -2.207000 57.18400 ymin,ymax (A): -23.58300 29.19700 zmin,zma (A): -9.685000 44.84200 x,y,z range (A): 59.39100 52.78000 54.52700 scale (grids/A): 1.798252 object centre (A): 27.48850 2.807000 17.57850 number of atom coordinates read : 3374 total number of charged atoms : 3227 net assigned charge : 5.500022 assigned positive charge : 506.0926 centred at (gu) : 95.86176 85.94538 90.51940 assigned negative charge : -500.5941 centred at (gu) : 95.91645 85.89172 90.60226 start vw surface at 0.1800000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 87012 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26822 grid for indexing accessible points = 1.400000 m= 29782 mr = 62298 m= 3787 mr = 21758 m= 155 mr = 2141 m= 2 mr = 49 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 1646 time to turn everything in is 0.7600000 number of dielectric boundary points 34492 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 198 iepsmp to db, and charging done at 0.9000000 number of grid points assigned charge 25193 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) : 0.5994174 object centre at (A) : 27.48850 2.807000 17.57850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.7166656E-03 -1.9991400E-02 midg,1,midg; midg,igrid,midg 7.4013253E-03 1.0959804E-02 1,midg,midg; igrid,midg,midg 2.8590633E-02 3.0804636E-02 gauss-seidel spectral radius is 0.9985400 estimated iterations to convergence 208 setup time was (sec) 1.060000 now iterating at: 13:59:33 rms-change max change #iterations 4.350991 171.1800 at 10iterations 1.986486 73.23128 at 20iterations 0.9052023 33.04762 at 30iterations 0.4146576 13.55023 at 40iterations 0.1891167 5.920464 at 50iterations 8.6494029E-02 2.715986 at 60iterations 3.9497357E-02 1.128062 at 70iterations 1.8109612E-02 0.5675945 at 80iterations 8.2979398E-03 0.2584190 at 90iterations 3.7967362E-03 0.1284561 at 100iterations 1.7415842E-03 5.2035332E-02 at 110iterations 7.9944008E-04 2.3270607E-02 at 120iterations finished qdiffx linear iterations at : 13:59:41 total time elapsed so far: 9.420000 # loops : 120 mean,max change (kT/e) : 7.9944008E-04 2.3270607E-02 energy calculations done at 9.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.590000 DelPhi exited at 13:59:42 9.589u 0.315s 0:10.35 95.5% 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 Mon Oct 10 2011 at 13:59:42 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3374 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.697378 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): -2.207000 57.18400 ymin,ymax (A): -23.58300 29.19700 zmin,zma (A): -9.685000 44.84200 x,y,z range (A): 59.39100 52.78000 54.52700 scale (grids/A): 2.697378 object centre (A): 27.48850 2.807000 17.57850 number of atom coordinates read : 3374 total number of charged atoms : 3227 net assigned charge : 5.500022 assigned positive charge : 506.0926 centred at (gu) : 98.79237 83.91785 90.77890 assigned negative charge : -500.5941 centred at (gu) : 98.87466 83.83743 90.90346 start vw surface at 0.1800000 fill in re-entrant regions at 0.6400000 boundary points on vw surface= 202136 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26822 grid for indexing accessible points = 1.400000 m= 99963 mr = 151335 m= 32275 mr = 81922 m= 6202 mr = 25348 m= 597 mr = 4447 m= 30 mr = 362 m= 0 mr = 2 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 5354 time to turn everything in is 1.910000 number of dielectric boundary points 77787 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.070000 number of grid points assigned charge 25811 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) : 1.798252 object centre at (A) : 27.48850 2.807000 17.57850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2491768E-02 -0.2318839 midg,1,midg; midg,igrid,midg 1.1092606E-02 0.1057303 1,midg,midg; igrid,midg,midg 0.3185962 0.3729643 gauss-seidel spectral radius is 0.9992464 estimated iterations to convergence 288 setup time was (sec) 2.240000 now iterating at: 13:59:44 rms-change max change #iterations 10.51990 285.4450 at 10iterations 6.145168 115.4900 at 20iterations 3.556492 74.01111 at 30iterations 2.058266 40.93666 at 40iterations 1.184619 22.62454 at 50iterations 0.6811424 13.37494 at 60iterations 0.3916710 7.407844 at 70iterations 0.2247936 4.505814 at 80iterations 0.1290979 2.298401 at 90iterations 7.3961489E-02 1.387768 at 100iterations 4.2338029E-02 0.7585316 at 110iterations 2.4245240E-02 0.4376583 at 120iterations 1.3922444E-02 0.2362366 at 130iterations 7.9974886E-03 0.1386383 at 140iterations 4.6056830E-03 8.3371162E-02 at 150iterations 2.6556288E-03 4.7134399E-02 at 160iterations 1.5365704E-03 2.6367188E-02 at 170iterations 8.9731131E-04 1.6269684E-02 at 180iterations finished qdiffx linear iterations at : 13:59:59 total time elapsed so far: 16.30000 # loops : 180 mean,max change (kT/e) : 8.9731131E-04 1.6269684E-02 energy calculations done at 16.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.48000 DelPhi exited at 13:59:59 16.481u 0.320s 0:17.18 97.7% 0+0k 0+0io 0pf+0w