Sat Oct 8 23:02:49 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 23:02:49 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2995 !!! WARNING: HIT 85 has a net charge of 0.5140 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 0.5574433 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): -15.66700 32.40000 ymin,ymax (A): 83.98800 147.8510 zmin,zma (A): 31.48000 87.38100 x,y,z range (A): 48.06700 63.86300 55.90100 scale (grids/A): 0.5574433 object centre (A): 8.366501 115.9195 59.43050 number of atom coordinates read : 2995 total number of charged atoms : 2852 net assigned charge : 5.240042 assigned positive charge : 442.4192 centred at (gu) : 90.45628 89.32518 90.74777 assigned negative charge : -437.1805 centred at (gu) : 90.41322 89.40533 90.89076 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6199 nv = 96 ne = 84 npr = 60184 no. pairs analyzed = 60184 no. exposed pairs = 3867 no. arc points = 27072 no. surface atoms = 1292 nbur = 1703 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 = 1.540000 m= 259 mr = 3251 m= 1 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 3198 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2745 ## 355 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 7997 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5907601E-09 -1.1316578E-09 midg,1,midg; midg,igrid,midg 1.5321354E-09 -2.4492228E-10 1,midg,midg; igrid,midg,midg 7.4850681E-11 1.0460190E-09 gauss-seidel spectral radius is 0.9834064 estimated iterations to convergence 64 setup time was (sec) 0.6500000 now iterating at: 23:02:50 rms-change max change #iterations 8.2701914E-02 13.77943 at 10iterations 5.9646247E-03 1.053532 at 20iterations 4.3693537E-04 8.0265045E-02 at 30iterations 3.4412751E-05 7.7981949E-03 at 40iterations 3.6112092E-06 6.6280365E-04 at 50iterations finished qdiffx linear iterations at : 23:02:53 total time elapsed so far: 3.920000 # loops : 50 mean,max change (kT/e) : 3.6112092E-06 6.6280365E-04 energy calculations done at 3.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.100000 DelPhi exited at 23:02:53 4.106u 0.255s 0:04.62 94.1% 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 Sat Oct 8 2011 at 23:02:54 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2995 !!! WARNING: HIT 85 has a net charge of 0.5140 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 1.672330 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): -15.66700 32.40000 ymin,ymax (A): 83.98800 147.8510 zmin,zma (A): 31.48000 87.38100 x,y,z range (A): 48.06700 63.86300 55.90100 scale (grids/A): 1.672330 object centre (A): 8.366501 115.9195 59.43050 number of atom coordinates read : 2995 total number of charged atoms : 2852 net assigned charge : 5.240042 assigned positive charge : 442.4192 centred at (gu) : 91.36810 87.97457 92.24276 assigned negative charge : -437.1805 centred at (gu) : 91.23975 88.21584 92.67212 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 68865 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27072 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 21973 mr = 47158 m= 2500 mr = 15298 m= 83 mr = 1218 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 228 time to turn everything in is 0.6100000 number of dielectric boundary points 29739 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 268 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 21970 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) : 0.5574433 object centre at (A) : 8.366501 115.9195 59.43050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2601005E-02 -9.9701365E-04 midg,1,midg; midg,igrid,midg 4.1174158E-02 1.4887678E-02 1,midg,midg; igrid,midg,midg -5.8709276E-03 1.2098228E-03 gauss-seidel spectral radius is 0.9982761 estimated iterations to convergence 191 setup time was (sec) 0.9200000 now iterating at: 23:02:55 rms-change max change #iterations 3.506931 143.3326 at 10iterations 1.490478 56.24380 at 20iterations 0.6339760 23.50357 at 30iterations 0.2707943 9.711771 at 40iterations 0.1153482 4.003408 at 50iterations 4.9138345E-02 1.796165 at 60iterations 2.0915469E-02 0.6994610 at 70iterations 8.9067016E-03 0.3102188 at 80iterations 3.8154470E-03 0.1353114 at 90iterations 1.6262889E-03 5.2046537E-02 at 100iterations 6.9550041E-04 2.4526596E-02 at 110iterations 2.9732587E-04 1.0273933E-02 at 120iterations finished qdiffx linear iterations at : 23:03:03 total time elapsed so far: 9.160000 # loops : 120 mean,max change (kT/e) : 2.9732587E-04 1.0273933E-02 energy calculations done at 9.160000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.340000 DelPhi exited at 23:03:03 9.343u 0.281s 0:09.93 96.8% 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 Sat Oct 8 2011 at 23:03:03 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: 317 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2995 !!! WARNING: HIT 85 has a net charge of 0.5140 !!! WARNING: TPO 1 has a net charge of -1.2740 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: 2.508495 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): -15.66700 32.40000 ymin,ymax (A): 83.98800 147.8510 zmin,zma (A): 31.48000 87.38100 x,y,z range (A): 48.06700 63.86300 55.90100 scale (grids/A): 2.508495 object centre (A): 8.366501 115.9195 59.43050 number of atom coordinates read : 2995 total number of charged atoms : 2852 net assigned charge : 5.240042 assigned positive charge : 442.4192 centred at (gu) : 92.05177 86.96170 93.36404 assigned negative charge : -437.1805 centred at (gu) : 91.85949 87.32381 94.00800 start vw surface at 0.1700000 fill in re-entrant regions at 0.5000000 boundary points on vw surface= 159743 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27072 grid for indexing accessible points = 1.400000 m= 74864 mr = 114965 m= 22450 mr = 59644 m= 3867 mr = 16845 m= 311 mr = 2496 m= 5 mr = 125 m= 0 mr = 0 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 763 time to turn everything in is 1.500000 number of dielectric boundary points 67165 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 22784 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) : 1.672330 object centre at (A) : 8.366501 115.9195 59.43050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3937440 -3.1245966E-02 midg,1,midg; midg,igrid,midg 0.7251529 0.2834976 1,midg,midg; igrid,midg,midg -7.5645484E-02 1.8600313E-02 gauss-seidel spectral radius is 0.9991662 estimated iterations to convergence 274 setup time was (sec) 1.830000 now iterating at: 23:03:06 rms-change max change #iterations 8.898096 304.3038 at 10iterations 5.027457 118.7262 at 20iterations 2.816380 59.17559 at 30iterations 1.575086 32.08118 at 40iterations 0.8777635 18.47969 at 50iterations 0.4877538 10.31416 at 60iterations 0.2718680 5.655109 at 70iterations 0.1506280 3.229919 at 80iterations 8.3850883E-02 1.666395 at 90iterations 4.6411566E-02 0.9588962 at 100iterations 2.5685366E-02 0.5575399 at 110iterations 1.4252543E-02 0.2993059 at 120iterations 7.9083191E-03 0.1546631 at 130iterations 4.3814424E-03 9.7072601E-02 at 140iterations 2.4262420E-03 4.8932076E-02 at 150iterations 1.3463000E-03 2.6195526E-02 at 160iterations 7.4721809E-04 1.4404297E-02 at 170iterations 4.1425848E-04 8.4438324E-03 at 180iterations finished qdiffx linear iterations at : 23:03:19 total time elapsed so far: 15.34000 # loops : 180 mean,max change (kT/e) : 4.1425848E-04 8.4438324E-03 energy calculations done at 15.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.51000 DelPhi exited at 23:03:20 15.512u 0.296s 0:16.09 98.1% 0+0k 0+0io 0pf+0w