Sat Oct 8 11:50:01 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 Sat Oct 8 2011 at 11:50:01 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3259 !!! WARNING: HIT 126 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5709978 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): -5.225000 53.09600 ymin,ymax (A): -11.09900 51.24800 zmin,zma (A): -10.35100 49.75800 x,y,z range (A): 58.32100 62.34700 60.10900 scale (grids/A): 0.5709978 object centre (A): 23.93550 20.07450 19.70350 number of atom coordinates read : 3259 total number of charged atoms : 3098 net assigned charge : -4.985986 assigned positive charge : 485.1393 centred at (gu) : 86.98096 91.30103 89.64428 assigned negative charge : -490.1267 centred at (gu) : 87.00185 91.32069 89.62350 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7160 nv = 96 ne = 84 npr = 63072 no. pairs analyzed = 63072 no. exposed pairs = 4665 no. arc points = 34049 no. surface atoms = 1542 nbur = 1717 mkacc time = 0.1600000 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 = 1.484000 m= 351 mr = 3361 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 4139 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3359 ## 367 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 9119 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2570353E-09 -3.9021236E-10 midg,1,midg; midg,igrid,midg -3.3185041E-10 -1.5442629E-09 1,midg,midg; igrid,midg,midg -8.2419011E-10 -5.7912392E-10 gauss-seidel spectral radius is 0.9842137 estimated iterations to convergence 65 setup time was (sec) 0.6700000 now iterating at: 11:50:02 rms-change max change #iterations 9.5608458E-02 15.44944 at 10iterations 7.1310210E-03 1.013996 at 20iterations 5.4031302E-04 9.4807625E-02 at 30iterations 4.6739595E-05 7.0180893E-03 at 40iterations 6.6746106E-06 1.0576248E-03 at 50iterations finished qdiffx linear iterations at : 11:50:06 total time elapsed so far: 4.420000 # loops : 50 mean,max change (kT/e) : 6.6746106E-06 1.0576248E-03 energy calculations done at 4.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.610000 DelPhi exited at 11:50:07 4.612u 0.381s 0:05.29 94.3% 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 Sat Oct 8 2011 at 11:50:07 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3259 !!! WARNING: HIT 126 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.712994 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): -5.225000 53.09600 ymin,ymax (A): -11.09900 51.24800 zmin,zma (A): -10.35100 49.75800 x,y,z range (A): 58.32100 62.34700 60.10900 scale (grids/A): 1.712994 object centre (A): 23.93550 20.07450 19.70350 number of atom coordinates read : 3259 total number of charged atoms : 3098 net assigned charge : -4.985986 assigned positive charge : 485.1393 centred at (gu) : 80.94179 93.90221 88.93143 assigned negative charge : -490.1267 centred at (gu) : 81.00510 93.96153 88.87002 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 77755 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34049 grid for indexing accessible points = 1.400000 m= 24005 mr = 49399 m= 2856 mr = 15510 m= 99 mr = 1358 m= 3 mr = 7 m= 0 mr = 0 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 33 time to turn everything in is 0.6400000 number of dielectric boundary points 38444 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 294 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 23982 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) : 0.5709978 object centre at (A) : 23.93550 20.07450 19.70350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.0004220E-02 9.2720256E-05 midg,1,midg; midg,igrid,midg 1.0435656E-02 -3.9776105E-02 1,midg,midg; igrid,midg,midg 2.2713498E-03 -3.6279571E-03 gauss-seidel spectral radius is 0.9984066 estimated iterations to convergence 199 setup time was (sec) 0.9500000 now iterating at: 11:50:08 rms-change max change #iterations 3.899236 189.3798 at 10iterations 1.706437 66.21378 at 20iterations 0.7513157 27.43899 at 30iterations 0.3314680 10.94100 at 40iterations 0.1455875 4.501813 at 50iterations 6.3919403E-02 2.259625 at 60iterations 2.8025270E-02 0.9561844 at 70iterations 1.2345036E-02 0.4337265 at 80iterations 5.4403157E-03 0.1814642 at 90iterations 2.3897297E-03 8.0965042E-02 at 100iterations 1.0529603E-03 3.6073685E-02 at 110iterations 4.6577663E-04 1.5655518E-02 at 120iterations finished qdiffx linear iterations at : 11:50:18 total time elapsed so far: 10.74000 # loops : 120 mean,max change (kT/e) : 4.6577663E-04 1.5655518E-02 energy calculations done at 10.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.91000 DelPhi exited at 11:50:18 10.919u 0.438s 0:11.69 97.0% 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 Sat Oct 8 2011 at 11:50:18 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: 308 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3259 !!! WARNING: HIT 126 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.569490 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): -5.225000 53.09600 ymin,ymax (A): -11.09900 51.24800 zmin,zma (A): -10.35100 49.75800 x,y,z range (A): 58.32100 62.34700 60.10900 scale (grids/A): 2.569490 object centre (A): 23.93550 20.07450 19.70350 number of atom coordinates read : 3259 total number of charged atoms : 3098 net assigned charge : -4.985986 assigned positive charge : 485.1393 centred at (gu) : 76.41254 95.85313 88.39675 assigned negative charge : -490.1267 centred at (gu) : 76.50755 95.94199 88.30486 start vw surface at 0.1300000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 180129 reading accessible surface arcs data from file ARCDAT no. of arc points read = 34049 grid for indexing accessible points = 1.400000 m= 80618 mr = 121515 m= 24422 mr = 61130 m= 4551 mr = 17636 m= 381 mr = 2892 m= 11 mr = 182 m= 0 mr = 0 time to grow re-entrant surface = 0.9800001 no. cavity mid-points inaccessible to solvent = 107 time to turn everything in is 1.610000 number of dielectric boundary points 86757 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 12 iepsmp to db, and charging done at 1.750000 number of grid points assigned charge 24773 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) : 1.712994 object centre at (A) : 23.93550 20.07450 19.70350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.7763572E-02 3.2676954E-02 midg,1,midg; midg,igrid,midg 0.3296284 -0.7556370 1,midg,midg; igrid,midg,midg -4.9516872E-02 -3.7431799E-02 gauss-seidel spectral radius is 0.9992365 estimated iterations to convergence 286 setup time was (sec) 1.950000 now iterating at: 11:50:21 rms-change max change #iterations 10.11123 399.6478 at 10iterations 5.988870 163.6713 at 20iterations 3.498843 88.82394 at 30iterations 2.039312 48.06114 at 40iterations 1.181423 27.11417 at 50iterations 0.6812167 18.59510 at 60iterations 0.3933179 8.582649 at 70iterations 0.2255587 4.659897 at 80iterations 0.1299090 3.480752 at 90iterations 7.4096598E-02 1.449001 at 100iterations 4.2420056E-02 0.8562555 at 110iterations 2.4275798E-02 0.4950173 at 120iterations 1.3847439E-02 0.3176575 at 130iterations 7.9027945E-03 0.1546936 at 140iterations 4.5083277E-03 8.9649200E-02 at 150iterations 2.5682019E-03 4.9672008E-02 at 160iterations 1.4662592E-03 2.8515816E-02 at 170iterations 8.3489728E-04 1.6288757E-02 at 180iterations finished qdiffx linear iterations at : 11:50:38 total time elapsed so far: 19.34000 # loops : 180 mean,max change (kT/e) : 8.3489728E-04 1.6288757E-02 energy calculations done at 19.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.51000 DelPhi exited at 11:50:39 19.515u 0.460s 0:20.29 98.4% 0+0k 0+0io 0pf+0w