Mon Oct 10 10:21:30 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 10:21:30 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2895 !!! WARNING: ASL 105 has a net charge of -0.1000 !!! WARNING: HIT 237 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: 0.5624812 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): 17.48200 74.33300 ymin,ymax (A): -44.12800 5.781000 zmin,zma (A): 7.661000 70.95200 x,y,z range (A): 56.85100 49.90900 63.29100 scale (grids/A): 0.5624812 object centre (A): 45.90750 -19.17350 39.30650 number of atom coordinates read : 2895 total number of charged atoms : 2745 net assigned charge : 8.914021 assigned positive charge : 426.8038 centred at (gu) : 92.14774 89.28651 89.23381 assigned negative charge : -417.8903 centred at (gu) : 92.40231 89.34859 89.17292 start vw surface at 0.1700000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6192 nv = 96 ne = 84 npr = 55774 no. pairs analyzed = 55774 no. exposed pairs = 4348 no. arc points = 31815 no. surface atoms = 1447 nbur = 1448 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 = 1.540000 m= 274 mr = 2706 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3300000 number of dielectric boundary points 3746 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3144 ## 399 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7889 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.8980076E-10 1.4911217E-09 midg,1,midg; midg,igrid,midg 2.1369146E-09 3.4449946E-10 1,midg,midg; igrid,midg,midg 2.3301399E-09 -3.2128029E-09 gauss-seidel spectral radius is 0.9837081 estimated iterations to convergence 64 setup time was (sec) 0.5800000 now iterating at: 10:21:31 rms-change max change #iterations 8.0090314E-02 13.50546 at 10iterations 5.7274192E-03 1.015099 at 20iterations 4.0455235E-04 6.8563461E-02 at 30iterations 3.0085612E-05 4.6014786E-03 at 40iterations 2.5383508E-06 4.9304962E-04 at 50iterations finished qdiffx linear iterations at : 10:21:34 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 2.5383508E-06 4.9304962E-04 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.590000 DelPhi exited at 10:21:34 3.591u 0.172s 0:04.03 93.3% 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 10:21:34 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: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2895 !!! WARNING: ASL 105 has a net charge of -0.1000 !!! WARNING: HIT 237 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: 1.687444 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): 17.48200 74.33300 ymin,ymax (A): -44.12800 5.781000 zmin,zma (A): 7.661000 70.95200 x,y,z range (A): 56.85100 49.90900 63.29100 scale (grids/A): 1.687444 object centre (A): 45.90750 -19.17350 39.30650 number of atom coordinates read : 2895 total number of charged atoms : 2745 net assigned charge : 8.914021 assigned positive charge : 426.8038 centred at (gu) : 96.44273 87.85907 87.70102 assigned negative charge : -417.8903 centred at (gu) : 97.20686 88.04556 87.51834 start vw surface at 0.1600000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 67105 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31815 grid for indexing accessible points = 1.400000 m= 20085 mr = 41063 m= 2245 mr = 12497 m= 83 mr = 939 m= 0 mr = 6 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5200000 number of dielectric boundary points 35013 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 274 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 21140 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) : 0.5624812 object centre at (A) : 45.90750 -19.17350 39.30650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3437139E-02 1.9296197E-02 midg,1,midg; midg,igrid,midg 9.4227791E-03 1.0877034E-02 1,midg,midg; igrid,midg,midg 2.4954066E-02 -1.3860557E-03 gauss-seidel spectral radius is 0.9983216 estimated iterations to convergence 194 setup time was (sec) 0.8300000 now iterating at: 10:21:35 rms-change max change #iterations 3.453154 152.7183 at 10iterations 1.478583 54.76852 at 20iterations 0.6355124 23.48378 at 30iterations 0.2730091 9.864643 at 40iterations 0.1175858 4.330746 at 50iterations 5.0232358E-02 1.719948 at 60iterations 2.1567114E-02 0.7747951 at 70iterations 9.3305856E-03 0.3585138 at 80iterations 4.0100212E-03 0.1534424 at 90iterations 1.7187450E-03 5.8922768E-02 at 100iterations 7.4243109E-04 2.8059006E-02 at 110iterations 3.1839643E-04 1.1119843E-02 at 120iterations finished qdiffx linear iterations at : 10:21:43 total time elapsed so far: 9.190000 # loops : 120 mean,max change (kT/e) : 3.1839643E-04 1.1119843E-02 energy calculations done at 9.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.380000 DelPhi exited at 10:21:44 9.383u 0.265s 0:10.02 96.2% 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 10:21:44 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 # of charge parameter records: 307 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2895 !!! WARNING: ASL 105 has a net charge of -0.1000 !!! WARNING: HIT 237 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: 2.531165 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): 17.48200 74.33300 ymin,ymax (A): -44.12800 5.781000 zmin,zma (A): 7.661000 70.95200 x,y,z range (A): 56.85100 49.90900 63.29100 scale (grids/A): 2.531165 object centre (A): 45.90750 -19.17350 39.30650 number of atom coordinates read : 2895 total number of charged atoms : 2745 net assigned charge : 8.914021 assigned positive charge : 426.8038 centred at (gu) : 99.66415 86.78845 86.55135 assigned negative charge : -417.8903 centred at (gu) : 100.8101 87.06836 86.27747 start vw surface at 0.1600000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 155109 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31815 grid for indexing accessible points = 1.400000 m= 67868 mr = 101249 m= 19917 mr = 50241 m= 3418 mr = 13929 m= 277 mr = 2016 m= 8 mr = 99 m= 0 mr = 2 time to grow re-entrant surface = 0.7000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.260000 number of dielectric boundary points 79061 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 21949 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) : 1.687444 object centre at (A) : 45.90750 -19.17350 39.30650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6284261 0.3315089 midg,1,midg; midg,igrid,midg 6.6809535E-02 0.1335005 1,midg,midg; igrid,midg,midg 0.3964613 3.5508550E-03 gauss-seidel spectral radius is 0.9991949 estimated iterations to convergence 278 setup time was (sec) 1.590000 now iterating at: 10:21:46 rms-change max change #iterations 8.999983 383.4144 at 10iterations 5.226202 135.3203 at 20iterations 3.003111 104.4933 at 30iterations 1.714782 49.36544 at 40iterations 0.9762094 22.88601 at 50iterations 0.5534910 14.34177 at 60iterations 0.3126735 6.969063 at 70iterations 0.1759588 3.652901 at 80iterations 9.9229731E-02 2.109371 at 90iterations 5.5737440E-02 1.214121 at 100iterations 3.1400651E-02 0.7126936 at 110iterations 1.7612092E-02 0.3878317 at 120iterations 9.8781874E-03 0.1978464 at 130iterations 5.5427402E-03 0.1153190 at 140iterations 3.1110835E-03 6.0523987E-02 at 150iterations 1.7400736E-03 3.9276123E-02 at 160iterations 9.7646174E-04 2.0128250E-02 at 170iterations 5.4819073E-04 1.1448860E-02 at 180iterations finished qdiffx linear iterations at : 10:21:57 total time elapsed so far: 12.63000 # loops : 180 mean,max change (kT/e) : 5.4819073E-04 1.1448860E-02 energy calculations done at 12.63000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.82000 DelPhi exited at 10:21:58 12.826u 0.287s 0:13.45 97.3% 0+0k 0+0io 0pf+0w