Mon Oct 10 09:24:46 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 09:24:46 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 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: 0.6117679 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): -9.094000 49.09800 ymin,ymax (A): 8.638000 47.78400 zmin,zma (A): -3.764000 38.85900 x,y,z range (A): 58.19200 39.14600 42.62300 scale (grids/A): 0.6117679 object centre (A): 20.00200 28.21100 17.54750 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 5.000010 assigned positive charge : 292.5479 centred at (gu) : 90.18750 89.69460 90.53931 assigned negative charge : -287.5482 centred at (gu) : 90.15909 89.61774 90.64420 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 4998 nv = 96 ne = 84 npr = 39623 no. pairs analyzed = 39623 no. exposed pairs = 2446 no. arc points = 17332 no. surface atoms = 830 nbur = 1136 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 220 mr = 2748 m= 3 mr = 13 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.2400000 number of dielectric boundary points 2460 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1730 ## 199 charges are in solution ## iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 6022 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.3576095E-09 -1.0948223E-09 midg,1,midg; midg,igrid,midg 1.5786260E-10 5.7042446E-09 1,midg,midg; igrid,midg,midg 1.9752557E-09 4.4294248E-09 gauss-seidel spectral radius is 0.9861141 estimated iterations to convergence 70 setup time was (sec) 0.5100000 now iterating at: 09:24:47 rms-change max change #iterations 0.1065419 20.90315 at 10iterations 9.3628597E-03 1.636112 at 20iterations 8.4567658E-04 0.1367931 at 30iterations 7.4372925E-05 1.3108253E-02 at 40iterations 6.6000048E-06 1.0652542E-03 at 50iterations finished qdiffx linear iterations at : 09:24:50 total time elapsed so far: 3.760000 # loops : 50 mean,max change (kT/e) : 6.6000048E-06 1.0652542E-03 energy calculations done at 3.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.950000 DelPhi exited at 09:24:51 3.949u 0.220s 0:04.48 92.8% 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 09:24:51 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 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: 1.835304 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): -9.094000 49.09800 ymin,ymax (A): 8.638000 47.78400 zmin,zma (A): -3.764000 38.85900 x,y,z range (A): 58.19200 39.14600 42.62300 scale (grids/A): 1.835304 object centre (A): 20.00200 28.21100 17.54750 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 5.000010 assigned positive charge : 292.5479 centred at (gu) : 90.56234 89.08349 91.61812 assigned negative charge : -287.5482 centred at (gu) : 90.47739 88.85332 91.93279 start vw surface at 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 54212 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17332 grid for indexing accessible points = 1.400000 m= 18309 mr = 37000 m= 2346 mr = 13672 m= 81 mr = 1404 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 1587 time to turn everything in is 0.4000000 number of dielectric boundary points 22861 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 154 iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 14374 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) : 0.6117679 object centre at (A) : 20.00200 28.21100 17.54750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.0878950E-03 -1.7482084E-03 midg,1,midg; midg,igrid,midg 2.4310809E-03 7.3094950E-03 1,midg,midg; igrid,midg,midg 2.1293955E-02 4.2059638E-02 gauss-seidel spectral radius is 0.9984565 estimated iterations to convergence 202 setup time was (sec) 0.7400000 now iterating at: 09:24:52 rms-change max change #iterations 3.347951 157.3371 at 10iterations 1.489740 56.96519 at 20iterations 0.6618637 24.51262 at 30iterations 0.2962250 11.50498 at 40iterations 0.1326075 5.350712 at 50iterations 5.9152283E-02 2.111228 at 60iterations 2.6225708E-02 1.065786 at 70iterations 1.1749252E-02 0.4171991 at 80iterations 5.2377088E-03 0.2045317 at 90iterations 2.3407002E-03 9.3494415E-02 at 100iterations 1.0451408E-03 4.0963650E-02 at 110iterations 4.6735723E-04 1.6561508E-02 at 120iterations finished qdiffx linear iterations at : 09:24:59 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 4.6735723E-04 1.6561508E-02 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.990000 DelPhi exited at 09:24:59 7.997u 0.307s 0:08.59 96.5% 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 09:24:59 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 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: 2.752956 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): -9.094000 49.09800 ymin,ymax (A): 8.638000 47.78400 zmin,zma (A): -3.764000 38.85900 x,y,z range (A): 58.19200 39.14600 42.62300 scale (grids/A): 2.752956 object centre (A): 20.00200 28.21100 17.54750 number of atom coordinates read : 1966 total number of charged atoms : 1834 net assigned charge : 5.000010 assigned positive charge : 292.5479 centred at (gu) : 90.84363 88.62537 92.42711 assigned negative charge : -287.5482 centred at (gu) : 90.71622 88.27993 92.89918 start vw surface at 0.1400000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 125415 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17332 grid for indexing accessible points = 1.400000 m= 60983 mr = 89882 m= 20214 mr = 50133 m= 3940 mr = 16331 m= 377 mr = 2926 m= 8 mr = 206 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 5527 time to turn everything in is 0.9800000 number of dielectric boundary points 51459 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 1.120000 number of grid points assigned charge 14664 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) : 1.835304 object centre at (A) : 20.00200 28.21100 17.54750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9602877E-02 5.0282567E-03 midg,1,midg; midg,igrid,midg 4.3312941E-02 6.0088947E-02 1,midg,midg; igrid,midg,midg 0.2404665 0.4841450 gauss-seidel spectral radius is 0.9991908 estimated iterations to convergence 278 setup time was (sec) 1.330000 now iterating at: 09:25:01 rms-change max change #iterations 8.057512 324.2467 at 10iterations 4.572703 116.7036 at 20iterations 2.577015 60.23579 at 30iterations 1.446361 32.47209 at 40iterations 0.8124097 17.82347 at 50iterations 0.4532790 10.49587 at 60iterations 0.2545119 5.543860 at 70iterations 0.1423528 3.097923 at 80iterations 7.9630636E-02 1.641663 at 90iterations 4.4460163E-02 0.9424438 at 100iterations 2.4891259E-02 0.5565853 at 110iterations 1.3883976E-02 0.3042545 at 120iterations 7.7836458E-03 0.1650066 at 130iterations 4.3487772E-03 8.9904785E-02 at 140iterations 2.4332632E-03 5.0666809E-02 at 150iterations 1.3590119E-03 2.9311180E-02 at 160iterations 7.6009688E-04 1.5989304E-02 at 170iterations 4.2492436E-04 9.9830627E-03 at 180iterations finished qdiffx linear iterations at : 09:25:13 total time elapsed so far: 13.63000 # loops : 180 mean,max change (kT/e) : 4.2492436E-04 9.9830627E-03 energy calculations done at 13.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.81000 DelPhi exited at 09:25:14 13.816u 0.311s 0:14.42 97.9% 0+0k 0+0io 0pf+0w