Mon Oct 10 16:03:19 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 16:03:19 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4778 !!! WARNING: GLM 134 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5400075 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): -19.60500 46.32000 ymin,ymax (A): 8.046000 73.08400 zmin,zma (A): 34.72600 94.95200 x,y,z range (A): 65.92500 65.03800 60.22601 scale (grids/A): 0.5400075 object centre (A): 13.35750 40.56500 64.83900 number of atom coordinates read : 4778 total number of charged atoms : 4615 net assigned charge : 3.906014 assigned positive charge : 719.2276 centred at (gu) : 90.35413 91.01241 89.91725 assigned negative charge : -715.3260 centred at (gu) : 90.36211 90.96272 89.91743 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8863 nv = 96 ne = 84 npr = 98309 no. pairs analyzed = 98309 no. exposed pairs = 5829 no. arc points = 38958 no. surface atoms = 1972 nbur = 2806 mkacc time = 0.1700000 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 = 1.596000 m= 353 mr = 4854 m= 3 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 4345 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4020 ## 515 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 11869 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9260661E-10 1.8200746E-10 midg,1,midg; midg,igrid,midg -1.8339084E-10 7.8525952E-10 1,midg,midg; igrid,midg,midg 2.3407082E-10 1.2941856E-10 gauss-seidel spectral radius is 0.9824506 estimated iterations to convergence 62 setup time was (sec) 0.5100000 now iterating at: 16:03:20 rms-change max change #iterations 9.0422578E-02 12.30911 at 10iterations 6.8515497E-03 0.9634762 at 20iterations 1.3175017E-03 0.2105370 at 30iterations 5.0214637E-04 7.0091248E-02 at 40iterations 2.2193088E-04 2.6449203E-02 at 50iterations finished qdiffx linear iterations at : 16:03:23 total time elapsed so far: 3.430000 # loops : 50 mean,max change (kT/e) : 2.2193088E-04 2.6449203E-02 energy calculations done at 3.430000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.570000 DelPhi exited at 16:03:23 3.571u 0.186s 0:04.07 92.1% 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 16:03:23 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4778 !!! WARNING: GLM 134 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.620023 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): -19.60500 46.32000 ymin,ymax (A): 8.046000 73.08400 zmin,zma (A): 34.72600 94.95200 x,y,z range (A): 65.92500 65.03800 60.22601 scale (grids/A): 1.620023 object centre (A): 13.35750 40.56500 64.83900 number of atom coordinates read : 4778 total number of charged atoms : 4615 net assigned charge : 3.906014 assigned positive charge : 719.2276 centred at (gu) : 91.06089 93.03553 89.75003 assigned negative charge : -715.3260 centred at (gu) : 91.08572 92.88769 89.75182 start vw surface at 0.1300000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 99626 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38958 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 31721 mr = 70855 m= 3408 mr = 21981 m= 100 mr = 1653 m= 0 mr = 7 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 224 time to turn everything in is 0.4800000 number of dielectric boundary points 40359 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 448 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5600000 number of grid points assigned charge 35263 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) : 0.5400075 object centre at (A) : 13.35750 40.56500 64.83900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.3240970E-03 1.1351250E-02 midg,1,midg; midg,igrid,midg -8.1604291E-03 -4.4721615E-05 1,midg,midg; igrid,midg,midg -2.7204985E-02 1.0365144E-02 gauss-seidel spectral radius is 0.9983301 estimated iterations to convergence 194 setup time was (sec) 0.7000000 now iterating at: 16:03:24 rms-change max change #iterations 4.306584 146.3220 at 10iterations 1.862750 66.36609 at 20iterations 0.8043947 25.30625 at 30iterations 0.3486705 10.96246 at 40iterations 0.1509165 4.359411 at 50iterations 6.5458581E-02 1.882652 at 60iterations 2.8648971E-02 0.8599014 at 70iterations 1.2599179E-02 0.3872619 at 80iterations 5.7145883E-03 0.1853867 at 90iterations 2.7618145E-03 8.9408875E-02 at 100iterations 1.5039312E-03 4.5465469E-02 at 110iterations 9.4869855E-04 2.5787354E-02 at 120iterations finished qdiffx linear iterations at : 16:03:31 total time elapsed so far: 8.030000 # loops : 120 mean,max change (kT/e) : 9.4869855E-04 2.5787354E-02 energy calculations done at 8.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.160000 DelPhi exited at 16:03:32 8.163u 0.219s 0:08.65 96.7% 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 16:03:32 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4778 !!! WARNING: GLM 134 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.430034 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): -19.60500 46.32000 ymin,ymax (A): 8.046000 73.08400 zmin,zma (A): 34.72600 94.95200 x,y,z range (A): 65.92500 65.03800 60.22601 scale (grids/A): 2.430034 object centre (A): 13.35750 40.56500 64.83900 number of atom coordinates read : 4778 total number of charged atoms : 4615 net assigned charge : 3.906014 assigned positive charge : 719.2276 centred at (gu) : 91.59097 94.55306 89.62465 assigned negative charge : -715.3260 centred at (gu) : 91.62849 94.33144 89.62764 start vw surface at 0.1300000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 232266 reading accessible surface arcs data from file ARCDAT no. of arc points read = 38958 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 110425 mr = 173558 m= 31693 mr = 87840 m= 5169 mr = 23688 m= 341 mr = 3374 m= 5 mr = 138 m= 0 mr = 0 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 803 time to turn everything in is 1.210000 number of dielectric boundary points 91301 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 1.320000 number of grid points assigned charge 36871 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) : 1.620023 object centre at (A) : 13.35750 40.56500 64.83900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6146950E-02 0.1926278 midg,1,midg; midg,igrid,midg -0.1596036 7.9454891E-03 1,midg,midg; igrid,midg,midg -0.5846702 0.1517091 gauss-seidel spectral radius is 0.9992211 estimated iterations to convergence 283 setup time was (sec) 1.480000 now iterating at: 16:03:34 rms-change max change #iterations 11.16806 377.3972 at 10iterations 6.555852 181.8167 at 20iterations 3.816360 88.11272 at 30iterations 2.213436 50.69452 at 40iterations 1.277936 24.67192 at 50iterations 0.7354741 14.80531 at 60iterations 0.4224795 7.578594 at 70iterations 0.2418449 4.689996 at 80iterations 0.1384788 2.364334 at 90iterations 7.9008915E-02 1.404598 at 100iterations 4.5067448E-02 0.8354042 at 110iterations 2.5822179E-02 0.4647213 at 120iterations 1.4781734E-02 0.2585258 at 130iterations 8.5087167E-03 0.1492615 at 140iterations 4.9666185E-03 9.7227097E-02 at 150iterations 2.9535750E-03 5.4075241E-02 at 160iterations 1.8300130E-03 3.1131744E-02 at 170iterations 1.2077272E-03 2.0980835E-02 at 180iterations finished qdiffx linear iterations at : 16:03:46 total time elapsed so far: 13.56000 # loops : 180 mean,max change (kT/e) : 1.2077272E-03 2.0980835E-02 energy calculations done at 13.56000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.69000 DelPhi exited at 16:03:46 13.693u 0.212s 0:14.18 98.0% 0+0k 0+0io 0pf+0w