Mon Oct 10 09:45:31 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 09:45:32 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2888 !!! WARNING: HIT 235 has a net charge of 0.5140 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: 0.5631486 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): 111.3700 174.5860 ymin,ymax (A): -44.13800 7.668000 zmin,zma (A): 48.63200 102.5880 x,y,z range (A): 63.21600 51.80600 53.95601 scale (grids/A): 0.5631486 object centre (A): 142.9780 -18.23500 75.61000 number of atom coordinates read : 2888 total number of charged atoms : 2738 net assigned charge : 6.014016 assigned positive charge : 425.8658 centred at (gu) : 89.49084 88.43711 88.87360 assigned negative charge : -419.8523 centred at (gu) : 89.52485 88.48299 88.74147 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6156 nv = 96 ne = 84 npr = 56002 no. pairs analyzed = 56002 no. exposed pairs = 4283 no. arc points = 30732 no. surface atoms = 1430 nbur = 1458 mkacc time = 0.1900000 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 = 1.512000 m= 303 mr = 2721 m= 0 mr = 18 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4200000 number of dielectric boundary points 3720 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3008 ## 348 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 7817 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1204704E-09 1.7096113E-09 midg,1,midg; midg,igrid,midg 1.8286930E-09 1.3741595E-10 1,midg,midg; igrid,midg,midg 1.2632320E-09 2.9273872E-10 gauss-seidel spectral radius is 0.9837419 estimated iterations to convergence 64 setup time was (sec) 0.7600000 now iterating at: 09:45:33 rms-change max change #iterations 8.7597534E-02 16.40742 at 10iterations 6.1532031E-03 1.022773 at 20iterations 4.4479643E-04 7.4407578E-02 at 30iterations 3.3599877E-05 5.1708221E-03 at 40iterations 3.3031772E-06 4.4155121E-04 at 50iterations finished qdiffx linear iterations at : 09:45:36 total time elapsed so far: 4.340000 # loops : 50 mean,max change (kT/e) : 3.3031772E-06 4.4155121E-04 energy calculations done at 4.340000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.560000 DelPhi exited at 09:45:37 4.568u 0.389s 0:05.72 86.3% 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 09:45:37 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2888 !!! WARNING: HIT 235 has a net charge of 0.5140 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: 1.689446 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): 111.3700 174.5860 ymin,ymax (A): -44.13800 7.668000 zmin,zma (A): 48.63200 102.5880 x,y,z range (A): 63.21600 51.80600 53.95601 scale (grids/A): 1.689446 object centre (A): 142.9780 -18.23500 75.61000 number of atom coordinates read : 2888 total number of charged atoms : 2738 net assigned charge : 6.014016 assigned positive charge : 425.8658 centred at (gu) : 88.47185 85.31046 86.62052 assigned negative charge : -419.8523 centred at (gu) : 88.57420 85.44859 86.22392 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 66317 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30732 grid for indexing accessible points = 1.400000 m= 20983 mr = 41034 m= 2828 mr = 13294 m= 130 mr = 1378 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.3500000 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 0.6800000 number of dielectric boundary points 34542 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 265 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 21149 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) : 0.5631486 object centre at (A) : 142.9780 -18.23500 75.61000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.1719815E-03 2.0139428E-02 midg,1,midg; midg,igrid,midg 1.5696477E-02 4.8158690E-03 1,midg,midg; igrid,midg,midg 2.3793818E-02 8.2616061E-03 gauss-seidel spectral radius is 0.9983220 estimated iterations to convergence 194 setup time was (sec) 1.010000 now iterating at: 09:45:39 rms-change max change #iterations 3.530500 150.5753 at 10iterations 1.512115 61.79890 at 20iterations 0.6533027 23.65940 at 30iterations 0.2816516 9.740561 at 40iterations 0.1213655 4.177838 at 50iterations 5.1961761E-02 2.047731 at 60iterations 2.2478184E-02 0.8001180 at 70iterations 9.6873660E-03 0.3604152 at 80iterations 4.1831373E-03 0.1538863 at 90iterations 1.7984249E-03 6.7061424E-02 at 100iterations 7.7397597E-04 3.0244827E-02 at 110iterations 3.3323400E-04 1.2782097E-02 at 120iterations finished qdiffx linear iterations at : 09:45:48 total time elapsed so far: 10.04000 # loops : 120 mean,max change (kT/e) : 3.3323400E-04 1.2782097E-02 energy calculations done at 10.04000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.25000 DelPhi exited at 09:45:48 10.252u 0.474s 0:11.01 97.3% 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 09:45:48 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: 299 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2888 !!! WARNING: HIT 235 has a net charge of 0.5140 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: 2.534168 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): 111.3700 174.5860 ymin,ymax (A): -44.13800 7.668000 zmin,zma (A): 48.63200 102.5880 x,y,z range (A): 63.21600 51.80600 53.95601 scale (grids/A): 2.534168 object centre (A): 142.9780 -18.23500 75.61000 number of atom coordinates read : 2888 total number of charged atoms : 2738 net assigned charge : 6.014016 assigned positive charge : 425.8658 centred at (gu) : 87.70780 82.96558 84.93056 assigned negative charge : -419.8523 centred at (gu) : 87.86119 83.17285 84.33575 start vw surface at 0.1600000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 153396 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30732 grid for indexing accessible points = 1.400000 m= 68768 mr = 101103 m= 22320 mr = 51356 m= 4447 mr = 16028 m= 420 mr = 2798 m= 10 mr = 195 m= 0 mr = 0 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 113 time to turn everything in is 1.730000 number of dielectric boundary points 77881 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.960000 number of grid points assigned charge 21891 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) : 1.689446 object centre at (A) : 142.9780 -18.23500 75.61000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.8274772E-02 0.2560454 midg,1,midg; midg,igrid,midg 0.2397778 0.1062365 1,midg,midg; igrid,midg,midg 0.3444275 9.5432639E-02 gauss-seidel spectral radius is 0.9991970 estimated iterations to convergence 279 setup time was (sec) 2.170000 now iterating at: 09:45:51 rms-change max change #iterations 9.175969 357.8959 at 10iterations 5.352843 163.3242 at 20iterations 3.081658 76.04991 at 30iterations 1.765538 43.42230 at 40iterations 1.006949 30.87122 at 50iterations 0.5724598 13.02466 at 60iterations 0.3237066 8.118301 at 70iterations 0.1830630 4.164850 at 80iterations 0.1034090 2.200678 at 90iterations 5.8207769E-02 1.292931 at 100iterations 3.2754339E-02 0.6265159 at 110iterations 1.8419368E-02 0.3767281 at 120iterations 1.0337468E-02 0.2199898 at 130iterations 5.8203926E-03 0.1235204 at 140iterations 3.2709856E-03 7.9698563E-02 at 150iterations 1.8341299E-03 3.8095474E-02 at 160iterations 1.0297021E-03 2.1476746E-02 at 170iterations 5.7826308E-04 1.3306141E-02 at 180iterations finished qdiffx linear iterations at : 09:46:06 total time elapsed so far: 17.54000 # loops : 180 mean,max change (kT/e) : 5.7826308E-04 1.3306141E-02 energy calculations done at 17.54000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.77000 DelPhi exited at 09:46:07 17.776u 0.460s 0:18.52 98.4% 0+0k 0+0io 0pf+0w