Wed Jan 25 17:37:40 PST 2012 #!/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 Wed Jan 25 2012 at 17:37:40 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2859 !!! WARNING: MG1 1111 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6011787 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): 9.770000 66.46300 ymin,ymax (A): 8.702001 65.40700 zmin,zma (A): 7.937000 67.15400 x,y,z range (A): 56.69300 56.70500 59.21700 scale (grids/A): 0.6011787 object centre (A): 38.11650 37.05450 37.54550 number of atom coordinates read : 2859 total number of charged atoms : 2716 net assigned charge : -3.599984 assigned positive charge : 427.7344 centred at (gu) : 89.62990 87.93923 88.32937 assigned negative charge : -431.3351 centred at (gu) : 89.61610 88.03460 88.34972 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7110 nv = 96 ne = 84 npr = 56054 no. pairs analyzed = 56054 no. exposed pairs = 3983 no. arc points = 28003 no. surface atoms = 1332 nbur = 1527 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 368 mr = 3647 m= 0 mr = 22 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3809 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2783 ## 280 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 8704 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.2019516E-09 -1.7583117E-09 midg,1,midg; midg,igrid,midg 3.6935197E-09 -3.5973611E-09 1,midg,midg; igrid,midg,midg -2.4653721E-09 -1.0331094E-09 gauss-seidel spectral radius is 0.9857128 estimated iterations to convergence 69 setup time was (sec) 0.4400000 now iterating at: 17:37:40 rms-change max change #iterations 0.1121811 19.22733 at 10iterations 9.5139556E-03 1.373413 at 20iterations 8.1979722E-04 0.1206131 at 30iterations 7.1518174E-05 1.0299683E-02 at 40iterations 6.8995255E-06 1.0738373E-03 at 50iterations finished qdiffx linear iterations at : 17:37:44 total time elapsed so far: 3.770000 # loops : 50 mean,max change (kT/e) : 6.8995255E-06 1.0738373E-03 energy calculations done at 3.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.910000 DelPhi exited at 17:37:44 3.915u 0.197s 0:04.40 93.1% 0+0k 0+45960io 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 Wed Jan 25 2012 at 17:37:44 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2859 !!! WARNING: MG1 1111 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.803536 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): 9.770000 66.46300 ymin,ymax (A): 8.702001 65.40700 zmin,zma (A): 7.937000 67.15400 x,y,z range (A): 56.69300 56.70500 59.21700 scale (grids/A): 1.803536 object centre (A): 38.11650 37.05450 37.54550 number of atom coordinates read : 2859 total number of charged atoms : 2716 net assigned charge : -3.599984 assigned positive charge : 427.7344 centred at (gu) : 88.88932 83.81670 84.98781 assigned negative charge : -431.3351 centred at (gu) : 88.84786 84.10336 85.04893 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 77499 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28003 grid for indexing accessible points = 1.400000 m= 26664 mr = 52012 m= 3538 mr = 18761 m= 132 mr = 1926 m= 0 mr = 20 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 90 time to turn everything in is 0.4900000 number of dielectric boundary points 35114 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 198 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 21222 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) : 0.6011787 object centre at (A) : 38.11650 37.05450 37.54550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.2924109E-02 -2.3832439E-02 midg,1,midg; midg,igrid,midg 9.2225820E-03 -5.2356841E-03 1,midg,midg; igrid,midg,midg -1.2183468E-02 -2.5339304E-02 gauss-seidel spectral radius is 0.9985156 estimated iterations to convergence 206 setup time was (sec) 0.7100000 now iterating at: 17:37:45 rms-change max change #iterations 4.031620 171.4817 at 10iterations 1.821594 63.39538 at 20iterations 0.8270787 30.45882 at 30iterations 0.3740813 11.88179 at 40iterations 0.1699498 5.472004 at 50iterations 7.6950662E-02 2.366318 at 60iterations 3.4965131E-02 1.035892 at 70iterations 1.5897805E-02 0.5599155 at 80iterations 7.2107012E-03 0.2369900 at 90iterations 3.2550755E-03 0.1012287 at 100iterations 1.4800946E-03 4.8736572E-02 at 110iterations 6.7375653E-04 2.0744324E-02 at 120iterations finished qdiffx linear iterations at : 17:37:52 total time elapsed so far: 7.960000 # loops : 120 mean,max change (kT/e) : 6.7375653E-04 2.0744324E-02 energy calculations done at 7.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.100000 DelPhi exited at 17:37:53 8.108u 0.205s 0:08.60 96.5% 0+0k 0+45288io 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 Wed Jan 25 2012 at 17:37:53 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 ! Automatically converted by prot2crg.py # of charge parameter records: 941 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2859 !!! WARNING: MG1 1111 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.705304 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): 9.770000 66.46300 ymin,ymax (A): 8.702001 65.40700 zmin,zma (A): 7.937000 67.15400 x,y,z range (A): 56.69300 56.70500 59.21700 scale (grids/A): 2.705304 object centre (A): 38.11650 37.05450 37.54550 number of atom coordinates read : 2859 total number of charged atoms : 2716 net assigned charge : -3.599984 assigned positive charge : 427.7344 centred at (gu) : 88.33386 80.72499 82.48138 assigned negative charge : -431.3351 centred at (gu) : 88.27179 81.15510 82.57325 start vw surface at 0.1000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 179485 reading accessible surface arcs data from file ARCDAT no. of arc points read = 28003 grid for indexing accessible points = 1.400000 m= 87443 mr = 126937 m= 29656 mr = 69630 m= 6217 mr = 22969 m= 574 mr = 4338 m= 21 mr = 262 m= 0 mr = 3 time to grow re-entrant surface = 0.8200001 no. cavity mid-points inaccessible to solvent = 279 time to turn everything in is 1.260000 number of dielectric boundary points 79257 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.350000 number of grid points assigned charge 21725 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) : 1.803536 object centre at (A) : 38.11650 37.05450 37.54550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.7648235E-02 -0.3159358 midg,1,midg; midg,igrid,midg 3.0746832E-02 -4.0414077E-03 1,midg,midg; igrid,midg,midg -0.1134655 -0.4021802 gauss-seidel spectral radius is 0.9992410 estimated iterations to convergence 287 setup time was (sec) 1.490000 now iterating at: 17:37:55 rms-change max change #iterations 9.776738 370.5834 at 10iterations 5.698055 117.5726 at 20iterations 3.302901 70.05565 at 30iterations 1.904770 39.93783 at 40iterations 1.092691 21.58716 at 50iterations 0.6267086 11.51966 at 60iterations 0.3595667 7.343307 at 70iterations 0.2052937 3.696323 at 80iterations 0.1174408 2.275988 at 90iterations 6.7052655E-02 1.241508 at 100iterations 3.8328461E-02 0.7255707 at 110iterations 2.1854073E-02 0.3947468 at 120iterations 1.2498319E-02 0.2231140 at 130iterations 7.1178437E-03 0.1404538 at 140iterations 4.0521654E-03 7.6145172E-02 at 150iterations 2.3116411E-03 4.5224190E-02 at 160iterations 1.3179093E-03 2.5807858E-02 at 170iterations 7.5284968E-04 1.3697624E-02 at 180iterations finished qdiffx linear iterations at : 17:38:06 total time elapsed so far: 12.99000 # loops : 180 mean,max change (kT/e) : 7.5284968E-04 1.3697624E-02 energy calculations done at 12.99000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.14000 DelPhi exited at 17:38:07 13.144u 0.227s 0:13.66 97.8% 0+0k 0+45280io 0pf+0w