Mon Oct 10 19:33:57 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+sph2.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 = amb2.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 19:33:57 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: 333 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2983 !!! WARNING: GLM 105 has a net charge of -0.0940 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: 0.5475913 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): -26.48100 29.36800 ymin,ymax (A): -19.94100 26.49000 zmin,zma (A): 9.105000 74.11700 x,y,z range (A): 55.84900 46.43100 65.01199 scale (grids/A): 0.5475913 object centre (A): 1.443500 3.274500 41.61100 number of atom coordinates read : 2983 total number of charged atoms : 2837 net assigned charge : -0.5939705 assigned positive charge : 447.4232 centred at (gu) : 89.62717 90.37120 89.82864 assigned negative charge : -448.0183 centred at (gu) : 89.64297 90.26576 89.85870 start vw surface at 9.0000004E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5845 nv = 96 ne = 84 npr = 58567 no. pairs analyzed = 58567 no. exposed pairs = 4045 no. arc points = 28783 no. surface atoms = 1325 nbur = 1658 mkacc time = 0.1000000 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= 276 mr = 2895 m= 3 mr = 14 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 0.2100000 number of dielectric boundary points 3215 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2938 ## 388 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 7731 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.7771502E-10 -2.4699096E-10 midg,1,midg; midg,igrid,midg -7.3219064E-10 7.6608569E-10 1,midg,midg; igrid,midg,midg 7.6229967E-11 -1.4194745E-10 gauss-seidel spectral radius is 0.9828118 estimated iterations to convergence 63 setup time was (sec) 0.4500000 now iterating at: 19:33:57 rms-change max change #iterations 7.4688204E-02 13.22446 at 10iterations 5.2547706E-03 0.8689194 at 20iterations 5.2801624E-04 9.2598438E-02 at 30iterations 1.1796263E-04 2.1841049E-02 at 40iterations 3.1937554E-05 6.0071945E-03 at 50iterations finished qdiffx linear iterations at : 19:34:01 total time elapsed so far: 3.570000 # loops : 50 mean,max change (kT/e) : 3.1937554E-05 6.0071945E-03 energy calculations done at 3.570000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.710000 DelPhi exited at 19:34:01 3.709u 0.222s 0:04.41 88.8% 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 19:34:01 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: 333 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2983 !!! WARNING: GLM 105 has a net charge of -0.0940 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: 1.642774 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): -26.48100 29.36800 ymin,ymax (A): -19.94100 26.49000 zmin,zma (A): 9.105000 74.11700 x,y,z range (A): 55.84900 46.43100 65.01199 scale (grids/A): 1.642774 object centre (A): 1.443500 3.274500 41.61100 number of atom coordinates read : 2983 total number of charged atoms : 2837 net assigned charge : -0.5939705 assigned positive charge : 447.4232 centred at (gu) : 88.88084 91.11301 89.48519 assigned negative charge : -448.0183 centred at (gu) : 88.92838 90.79698 89.57585 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 64024 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28783 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 20407 mr = 41878 m= 2399 mr = 13894 m= 76 mr = 1239 m= 0 mr = 7 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 29888 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 303 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 21792 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) : 0.5475913 object centre at (A) : 1.443500 3.274500 41.61100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.6737298E-03 -5.2862759E-03 midg,1,midg; midg,igrid,midg -4.6460326E-03 9.5306784E-03 1,midg,midg; igrid,midg,midg -4.2684432E-03 1.3607637E-04 gauss-seidel spectral radius is 0.9982193 estimated iterations to convergence 188 setup time was (sec) 0.6000000 now iterating at: 19:34:02 rms-change max change #iterations 3.380322 140.5524 at 10iterations 1.414954 55.75739 at 20iterations 0.5957423 22.30584 at 30iterations 0.2495150 9.252483 at 40iterations 0.1052359 3.449169 at 50iterations 4.4136494E-02 1.644415 at 60iterations 1.8581787E-02 0.6653471 at 70iterations 7.8353249E-03 0.3417664 at 80iterations 3.3317925E-03 0.1393374 at 90iterations 1.4293074E-03 5.3886414E-02 at 100iterations 6.2762055E-04 2.3035049E-02 at 110iterations 2.8882228E-04 1.2639999E-02 at 120iterations finished qdiffx linear iterations at : 19:34:10 total time elapsed so far: 8.500000 # loops : 120 mean,max change (kT/e) : 2.8882228E-04 1.2639999E-02 energy calculations done at 8.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.640000 DelPhi exited at 19:34:11 8.638u 0.275s 0:09.38 94.8% 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 19:34:11 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: 333 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2983 !!! WARNING: GLM 105 has a net charge of -0.0940 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: 2.464161 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): -26.48100 29.36800 ymin,ymax (A): -19.94100 26.49000 zmin,zma (A): 9.105000 74.11700 x,y,z range (A): 55.84900 46.43100 65.01199 scale (grids/A): 2.464161 object centre (A): 1.443500 3.274500 41.61100 number of atom coordinates read : 2983 total number of charged atoms : 2837 net assigned charge : -0.5939705 assigned positive charge : 447.4232 centred at (gu) : 88.32114 91.66934 89.22775 assigned negative charge : -448.0183 centred at (gu) : 88.39247 91.19547 89.36372 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 148533 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28783 grid for indexing accessible points = 1.400000 m= 68630 mr = 103147 m= 21120 mr = 53332 m= 3857 mr = 15815 m= 283 mr = 2626 m= 2 mr = 123 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8500000 number of dielectric boundary points 67382 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 22673 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) : 1.642774 object centre at (A) : 1.443500 3.274500 41.61100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.9080090E-02 3.0168515E-02 midg,1,midg; midg,igrid,midg -5.0620679E-02 0.1192154 1,midg,midg; igrid,midg,midg -1.1372857E-02 2.6204614E-02 gauss-seidel spectral radius is 0.9991530 estimated iterations to convergence 271 setup time was (sec) 1.140000 now iterating at: 19:34:12 rms-change max change #iterations 8.637525 392.3848 at 10iterations 4.818189 124.2845 at 20iterations 2.681703 71.95230 at 30iterations 1.494696 40.57182 at 40iterations 0.8300324 19.49489 at 50iterations 0.4601311 11.26036 at 60iterations 0.2553433 5.759134 at 70iterations 0.1413157 3.393188 at 80iterations 7.8403346E-02 1.746396 at 90iterations 4.3173630E-02 1.032146 at 100iterations 2.3965044E-02 0.5485859 at 110iterations 1.3255631E-02 0.2733459 at 120iterations 7.3279766E-03 0.1542492 at 130iterations 4.0621222E-03 0.1000748 at 140iterations 2.2540262E-03 4.9309731E-02 at 150iterations 1.2533797E-03 2.6575089E-02 at 160iterations 7.0038042E-04 1.5693784E-02 at 170iterations 3.9668250E-04 8.9988708E-03 at 180iterations finished qdiffx linear iterations at : 19:34:25 total time elapsed so far: 13.70000 # loops : 180 mean,max change (kT/e) : 3.9668250E-04 8.9988708E-03 energy calculations done at 13.70000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.83000 DelPhi exited at 19:34:25 13.834u 0.268s 0:14.52 97.0% 0+0k 0+0io 0pf+0w