Tue Oct 11 06:58:57 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 Tue Oct 11 2011 at 06:58:58 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2972 !!! WARNING: HIR 199 has a net charge of 0.5140 !!! WARNING: GLM 217 has a net charge of -0.0940 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 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: 0.5406308 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): -19.73700 46.11200 ymin,ymax (A): 21.47600 76.88500 zmin,zma (A): -71.67800 -23.23700 x,y,z range (A): 65.84900 55.40900 48.44100 scale (grids/A): 0.5406308 object centre (A): 13.18750 49.18050 -47.45750 number of atom coordinates read : 2972 total number of charged atoms : 2826 net assigned charge : -0.5409935 assigned positive charge : 435.3856 centred at (gu) : 88.99677 90.14088 89.93518 assigned negative charge : -435.9272 centred at (gu) : 89.03848 90.23552 89.93701 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 5608 nv = 96 ne = 84 npr = 61252 no. pairs analyzed = 61252 no. exposed pairs = 3694 no. arc points = 26136 no. surface atoms = 1255 nbur = 1717 mkacc time = 0.1300000 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 = 1.596000 m= 238 mr = 2912 m= 1 mr = 11 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 2924 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2602 ## 339 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7365 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9226174E-11 -3.7817707E-11 midg,1,midg; midg,igrid,midg 4.5251516E-10 -5.5810773E-10 1,midg,midg; igrid,midg,midg 2.4869332E-10 -1.9569053E-10 gauss-seidel spectral radius is 0.9823657 estimated iterations to convergence 62 setup time was (sec) 0.5300000 now iterating at: 06:58:58 rms-change max change #iterations 7.1234725E-02 12.12682 at 10iterations 4.8512644E-03 0.7381983 at 20iterations 4.0720869E-04 6.8426132E-02 at 30iterations 6.2846026E-05 1.5110016E-02 at 40iterations 1.3741595E-05 3.4084320E-03 at 50iterations finished qdiffx linear iterations at : 06:59:01 total time elapsed so far: 3.110000 # loops : 50 mean,max change (kT/e) : 1.3741595E-05 3.4084320E-03 energy calculations done at 3.110000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.280000 DelPhi exited at 06:59:01 3.287u 0.184s 0:03.78 91.5% 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 Tue Oct 11 2011 at 06:59:01 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2972 !!! WARNING: HIR 199 has a net charge of 0.5140 !!! WARNING: GLM 217 has a net charge of -0.0940 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 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: 1.621893 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): -19.73700 46.11200 ymin,ymax (A): 21.47600 76.88500 zmin,zma (A): -71.67800 -23.23700 x,y,z range (A): 65.84900 55.40900 48.44100 scale (grids/A): 1.621893 object centre (A): 13.18750 49.18050 -47.45750 number of atom coordinates read : 2972 total number of charged atoms : 2826 net assigned charge : -0.5409935 assigned positive charge : 435.3856 centred at (gu) : 86.98959 90.42196 89.80504 assigned negative charge : -435.9272 centred at (gu) : 87.11522 90.70611 89.81084 start vw surface at 0.1600000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 61834 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26136 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 18995 mr = 41459 m= 2017 mr = 13195 m= 30 mr = 1078 m= 1 mr = 2 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 0.4600000 number of dielectric boundary points 27143 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 290 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5800000 number of grid points assigned charge 21710 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) : 0.5406308 object centre at (A) : 13.18750 49.18050 -47.45750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1816196E-03 7.8992806E-03 midg,1,midg; midg,igrid,midg -3.9341995E-03 4.3410477E-03 1,midg,midg; igrid,midg,midg 4.3452429E-03 -2.2442866E-02 gauss-seidel spectral radius is 0.9981624 estimated iterations to convergence 185 setup time was (sec) 0.7500000 now iterating at: 06:59:02 rms-change max change #iterations 3.253871 168.8966 at 10iterations 1.347336 55.04633 at 20iterations 0.5598584 22.20393 at 30iterations 0.2320648 8.916263 at 40iterations 9.6621372E-02 3.709184 at 50iterations 4.0045992E-02 1.545125 at 60iterations 1.6657406E-02 0.5691376 at 70iterations 6.9402964E-03 0.2697945 at 80iterations 2.9235540E-03 0.1134317 at 90iterations 1.2306104E-03 4.8017502E-02 at 100iterations 5.2797608E-04 1.9668579E-02 at 110iterations 2.3673908E-04 9.7846985E-03 at 120iterations finished qdiffx linear iterations at : 06:59:09 total time elapsed so far: 7.140000 # loops : 120 mean,max change (kT/e) : 2.3673908E-04 9.7846985E-03 energy calculations done at 7.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.320000 DelPhi exited at 06:59:10 7.322u 0.209s 0:08.18 91.9% 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 Tue Oct 11 2011 at 06:59:10 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: 304 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2972 !!! WARNING: HIR 199 has a net charge of 0.5140 !!! WARNING: GLM 217 has a net charge of -0.0940 !!! WARNING: SEP 219 has a net charge of -0.4750 !!! WARNING: HIR 259 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.432839 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): -19.73700 46.11200 ymin,ymax (A): 21.47600 76.88500 zmin,zma (A): -71.67800 -23.23700 x,y,z range (A): 65.84900 55.40900 48.44100 scale (grids/A): 2.432839 object centre (A): 13.18750 49.18050 -47.45750 number of atom coordinates read : 2972 total number of charged atoms : 2826 net assigned charge : -0.5409935 assigned positive charge : 435.3856 centred at (gu) : 85.48431 90.63290 89.70729 assigned negative charge : -435.9272 centred at (gu) : 85.67273 91.05910 89.71615 start vw surface at 0.1600000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 143594 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26136 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 65548 mr = 101611 m= 19373 mr = 51925 m= 3121 mr = 14871 m= 199 mr = 2191 m= 4 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.5899999 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.070000 number of dielectric boundary points 61135 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 23 iepsmp to db, and charging done at 1.190000 number of grid points assigned charge 22574 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) : 1.621893 object centre at (A) : 13.18750 49.18050 -47.45750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.7531983E-02 0.1416781 midg,1,midg; midg,igrid,midg -6.4532012E-02 0.1234096 1,midg,midg; igrid,midg,midg -1.5574524E-02 -0.4941878 gauss-seidel spectral radius is 0.9991323 estimated iterations to convergence 268 setup time was (sec) 1.370000 now iterating at: 06:59:11 rms-change max change #iterations 8.394542 257.6183 at 10iterations 4.706655 112.3475 at 20iterations 2.626050 62.60751 at 30iterations 1.457199 31.49828 at 40iterations 0.8062629 18.30618 at 50iterations 0.4451140 9.430162 at 60iterations 0.2453254 5.466230 at 70iterations 0.1352566 2.814451 at 80iterations 7.4365571E-02 1.623832 at 90iterations 4.0782735E-02 0.9350414 at 100iterations 2.2429531E-02 0.4750738 at 110iterations 1.2306510E-02 0.2595091 at 120iterations 6.7511513E-03 0.1631188 at 130iterations 3.6946635E-03 7.8361511E-02 at 140iterations 2.0240869E-03 4.1186333E-02 at 150iterations 1.1123436E-03 2.4650574E-02 at 160iterations 6.0879771E-04 1.2825012E-02 at 170iterations 3.3356785E-04 6.7892075E-03 at 180iterations finished qdiffx linear iterations at : 06:59:21 total time elapsed so far: 11.52000 # loops : 180 mean,max change (kT/e) : 3.3356785E-04 6.7892075E-03 energy calculations done at 11.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.69000 DelPhi exited at 06:59:22 11.695u 0.216s 0:12.42 95.8% 0+0k 0+0io 0pf+0w