Sat Oct 8 15:21:12 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+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 Sat Oct 8 2011 at 15:21:12 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3253 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: 0.6097874 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): -61.01500 -2.634000 ymin,ymax (A): -26.39200 25.85300 zmin,zma (A): -10.30300 45.09400 x,y,z range (A): 58.38100 52.24500 55.39700 scale (grids/A): 0.6097874 object centre (A): -31.82450 -0.2694998 17.39550 number of atom coordinates read : 3253 total number of charged atoms : 3108 net assigned charge : 5.500021 assigned positive charge : 486.1987 centred at (gu) : 91.66429 89.24770 90.78996 assigned negative charge : -480.7001 centred at (gu) : 91.70493 89.27873 90.79446 start vw surface at 0.1600000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7944 nv = 96 ne = 84 npr = 67354 no. pairs analyzed = 67354 no. exposed pairs = 3660 no. arc points = 25800 no. surface atoms = 1239 nbur = 2014 mkacc time = 0.1900000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 370 mr = 4560 m= 0 mr = 36 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 3718 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2640 ## 273 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 9999 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.9647285E-09 3.5236807E-09 midg,1,midg; midg,igrid,midg 6.0479239E-09 1.1662100E-09 1,midg,midg; igrid,midg,midg 3.9565009E-09 1.0329163E-09 gauss-seidel spectral radius is 0.9861263 estimated iterations to convergence 70 setup time was (sec) 0.7000000 now iterating at: 15:21:13 rms-change max change #iterations 0.1286789 15.52540 at 10iterations 1.1980979E-02 1.600163 at 20iterations 1.0750577E-03 0.1536846 at 30iterations 1.0033893E-04 1.2710571E-02 at 40iterations 1.0626924E-05 1.4381409E-03 at 50iterations finished qdiffx linear iterations at : 15:21:17 total time elapsed so far: 4.110000 # loops : 50 mean,max change (kT/e) : 1.0626924E-05 1.4381409E-03 energy calculations done at 4.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.300000 DelPhi exited at 15:21:17 4.303u 0.293s 0:04.90 93.6% 0+0k 0+0io 6pf+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 15:21:17 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3253 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: 1.829362 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): -61.01500 -2.634000 ymin,ymax (A): -26.39200 25.85300 zmin,zma (A): -10.30300 45.09400 x,y,z range (A): 58.38100 52.24500 55.39700 scale (grids/A): 1.829362 object centre (A): -31.82450 -0.2694998 17.39550 number of atom coordinates read : 3253 total number of charged atoms : 3108 net assigned charge : 5.500021 assigned positive charge : 486.1987 centred at (gu) : 94.99209 87.74218 92.36899 assigned negative charge : -480.7001 centred at (gu) : 95.11465 87.83576 92.38305 start vw surface at 0.1800000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 87800 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25800 grid for indexing accessible points = 1.400000 m= 30562 mr = 63265 m= 4035 mr = 22701 m= 157 mr = 2388 m= 0 mr = 27 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 2356 time to turn everything in is 0.7600000 number of dielectric boundary points 34173 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 209 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 24313 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) : 0.6097874 object centre at (A) : -31.82450 -0.2694998 17.39550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 7.8127664E-03 -1.7661631E-02 midg,1,midg; midg,igrid,midg 1.7657036E-02 1.0094863E-02 1,midg,midg; igrid,midg,midg 3.6803246E-02 1.7642256E-02 gauss-seidel spectral radius is 0.9985790 estimated iterations to convergence 210 setup time was (sec) 1.090000 now iterating at: 15:21:19 rms-change max change #iterations 4.417137 168.6578 at 10iterations 2.033567 66.31898 at 20iterations 0.9410253 29.03646 at 30iterations 0.4342651 13.03216 at 40iterations 0.2005660 5.968262 at 50iterations 9.2658550E-02 2.849854 at 60iterations 4.2841099E-02 1.167833 at 70iterations 1.9716563E-02 0.5639372 at 80iterations 9.1342023E-03 0.2899237 at 90iterations 4.2307898E-03 0.1284542 at 100iterations 1.9490108E-03 5.7088852E-02 at 110iterations 8.9905108E-04 2.7296066E-02 at 120iterations finished qdiffx linear iterations at : 15:21:27 total time elapsed so far: 9.850000 # loops : 120 mean,max change (kT/e) : 8.9905108E-04 2.7296066E-02 energy calculations done at 9.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.03000 DelPhi exited at 15:21:28 10.031u 0.321s 0:10.65 97.1% 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 15:21:28 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3253 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: 2.744043 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): -61.01500 -2.634000 ymin,ymax (A): -26.39200 25.85300 zmin,zma (A): -10.30300 45.09400 x,y,z range (A): 58.38100 52.24500 55.39700 scale (grids/A): 2.744043 object centre (A): -31.82450 -0.2694998 17.39550 number of atom coordinates read : 3253 total number of charged atoms : 3108 net assigned charge : 5.500021 assigned positive charge : 486.1987 centred at (gu) : 97.48783 86.61307 93.55326 assigned negative charge : -480.7001 centred at (gu) : 97.67182 86.75354 93.57448 start vw surface at 0.1900000 fill in re-entrant regions at 0.6600000 boundary points on vw surface= 203605 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25800 grid for indexing accessible points = 1.400000 m= 102501 mr = 153222 m= 33762 mr = 84790 m= 6823 mr = 26886 m= 673 mr = 5047 m= 15 mr = 378 m= 0 mr = 2 time to grow re-entrant surface = 1.160000 no. cavity mid-points inaccessible to solvent = 8092 time to turn everything in is 1.960000 number of dielectric boundary points 77054 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 2.120000 number of grid points assigned charge 24862 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) : 1.829362 object centre at (A) : -31.82450 -0.2694998 17.39550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8914486E-02 -0.1566552 midg,1,midg; midg,igrid,midg 7.4880742E-02 0.1197428 1,midg,midg; igrid,midg,midg 0.4684541 0.1986804 gauss-seidel spectral radius is 0.9992512 estimated iterations to convergence 288 setup time was (sec) 2.310000 now iterating at: 15:21:30 rms-change max change #iterations 10.42402 345.6815 at 10iterations 6.009359 112.6690 at 20iterations 3.455317 60.92703 at 30iterations 1.981549 35.54997 at 40iterations 1.137356 20.30717 at 50iterations 0.6512966 11.49631 at 60iterations 0.3738112 6.624569 at 70iterations 0.2139798 4.187073 at 80iterations 0.1222769 2.367622 at 90iterations 7.0221327E-02 1.169889 at 100iterations 4.0114593E-02 0.7035480 at 110iterations 2.2992112E-02 0.4076223 at 120iterations 1.3147406E-02 0.2202721 at 130iterations 7.5435317E-03 0.1381588 at 140iterations 4.3163556E-03 7.1994781E-02 at 150iterations 2.4740174E-03 4.1637421E-02 at 160iterations 1.4231147E-03 2.4978638E-02 at 170iterations 8.1566308E-04 1.3582230E-02 at 180iterations finished qdiffx linear iterations at : 15:21:45 total time elapsed so far: 16.92000 # loops : 180 mean,max change (kT/e) : 8.1566308E-04 1.3582230E-02 energy calculations done at 16.92000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.11000 DelPhi exited at 15:21:46 17.114u 0.324s 0:17.72 98.3% 0+0k 0+0io 0pf+0w