Tue Oct 11 08:26:25 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 08:26:25 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: 349 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2894 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: SEP 241 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 0.6586007 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): -15.10900 34.18400 ymin,ymax (A): 6.857000 55.46300 zmin,zma (A): 25.86600 79.92000 x,y,z range (A): 49.29300 48.60600 54.05400 scale (grids/A): 0.6586007 object centre (A): 9.537501 31.16000 52.89300 number of atom coordinates read : 2894 total number of charged atoms : 2739 net assigned charge : 1.701020 assigned positive charge : 443.4136 centred at (gu) : 90.05669 90.36050 88.95796 assigned negative charge : -441.7132 centred at (gu) : 90.31448 90.25146 88.96324 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8365 nv = 96 ne = 84 npr = 59278 no. pairs analyzed = 59278 no. exposed pairs = 3524 no. arc points = 24275 no. surface atoms = 1181 nbur = 1713 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 451 mr = 4764 m= 3 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 30 time to turn everything in is 0.3500000 number of dielectric boundary points 3986 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2390 ## 221 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 9987 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.5928281E-09 2.4745532E-09 midg,1,midg; midg,igrid,midg -1.8292063E-08 2.9761360E-08 1,midg,midg; igrid,midg,midg 5.7936880E-08 -5.3998594E-08 gauss-seidel spectral radius is 0.9880743 estimated iterations to convergence 75 setup time was (sec) 0.6500000 now iterating at: 08:26:26 rms-change max change #iterations 0.1772147 24.27668 at 10iterations 1.9808622E-02 2.856479 at 20iterations 2.3413314E-03 0.2693939 at 30iterations 4.0898367E-04 4.6379089E-02 at 40iterations 1.1487133E-04 1.2539864E-02 at 50iterations finished qdiffx linear iterations at : 08:26:30 total time elapsed so far: 4.720000 # loops : 50 mean,max change (kT/e) : 1.1487133E-04 1.2539864E-02 energy calculations done at 4.720000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.890000 DelPhi exited at 08:26:31 4.895u 0.357s 0:05.63 93.0% 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 08:26:31 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: 349 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2894 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: SEP 241 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 1.975802 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): -15.10900 34.18400 ymin,ymax (A): 6.857000 55.46300 zmin,zma (A): 25.86600 79.92000 x,y,z range (A): 49.29300 48.60600 54.05400 scale (grids/A): 1.975802 object centre (A): 9.537501 31.16000 52.89300 number of atom coordinates read : 2894 total number of charged atoms : 2739 net assigned charge : 1.701020 assigned positive charge : 443.4136 centred at (gu) : 90.16911 91.08090 86.87333 assigned negative charge : -441.7132 centred at (gu) : 90.94331 90.75390 86.88922 start vw surface at 0.1400000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 90262 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24275 grid for indexing accessible points = 1.400000 m= 34372 mr = 64267 m= 5776 mr = 25931 m= 405 mr = 3672 m= 3 mr = 178 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 1100 time to turn everything in is 0.7300000 number of dielectric boundary points 36770 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 154 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 21630 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) : 0.6586007 object centre at (A) : 9.537501 31.16000 52.89300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -7.9585537E-03 -2.8943654E-02 midg,1,midg; midg,igrid,midg -9.1033475E-03 1.8612716E-02 1,midg,midg; igrid,midg,midg 8.4179103E-02 -1.5617876E-02 gauss-seidel spectral radius is 0.9987567 estimated iterations to convergence 225 setup time was (sec) 1.060000 now iterating at: 08:26:33 rms-change max change #iterations 4.934441 243.5746 at 10iterations 2.397504 75.61194 at 20iterations 1.164862 32.55107 at 30iterations 0.5678191 15.38047 at 40iterations 0.2765709 8.269192 at 50iterations 0.1341745 3.780124 at 60iterations 6.5310307E-02 1.839442 at 70iterations 3.1811710E-02 1.021164 at 80iterations 1.5480496E-02 0.4246445 at 90iterations 7.5910497E-03 0.2422180 at 100iterations 3.7474153E-03 0.1148682 at 110iterations 1.8806095E-03 5.5120468E-02 at 120iterations finished qdiffx linear iterations at : 08:26:43 total time elapsed so far: 11.96000 # loops : 120 mean,max change (kT/e) : 1.8806095E-03 5.5120468E-02 energy calculations done at 11.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.13000 DelPhi exited at 08:26:44 12.135u 0.430s 0:13.23 94.9% 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 08:26:44 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: 349 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2894 !!! WARNING: HIR 79 has a net charge of 0.5140 !!! WARNING: SEP 241 has a net charge of -0.4750 !!! WARNING: TYS 1 has a net charge of -0.3380 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: 2.963703 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): -15.10900 34.18400 ymin,ymax (A): 6.857000 55.46300 zmin,zma (A): 25.86600 79.92000 x,y,z range (A): 49.29300 48.60600 54.05400 scale (grids/A): 2.963703 object centre (A): 9.537501 31.16000 52.89300 number of atom coordinates read : 2894 total number of charged atoms : 2739 net assigned charge : 1.701020 assigned positive charge : 443.4136 centred at (gu) : 90.25357 91.62139 85.30985 assigned negative charge : -441.7132 centred at (gu) : 91.41494 91.13071 85.33376 start vw surface at 0.1300000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 208395 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24275 grid for indexing accessible points = 1.400000 m= 110274 mr = 154756 m= 41408 mr = 91693 m= 10398 mr = 33763 m= 1697 mr = 7894 m= 130 mr = 1219 m= 3 mr = 57 m= 0 mr = 0 time to grow re-entrant surface = 1.200000 no. cavity mid-points inaccessible to solvent = 3706 time to turn everything in is 1.940000 number of dielectric boundary points 82923 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 2.080000 number of grid points assigned charge 21911 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) : 1.975802 object centre at (A) : 9.537501 31.16000 52.89300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1024291 -0.3558114 midg,1,midg; midg,igrid,midg -0.1002848 0.2282935 1,midg,midg; igrid,midg,midg 0.7429175 -0.1240433 gauss-seidel spectral radius is 0.9992920 estimated iterations to convergence 297 setup time was (sec) 2.290000 now iterating at: 08:26:47 rms-change max change #iterations 11.31399 364.5815 at 10iterations 6.676980 170.6665 at 20iterations 3.929516 84.12901 at 30iterations 2.306477 43.96107 at 40iterations 1.353050 24.10176 at 50iterations 0.7942896 15.83895 at 60iterations 0.4647933 8.116312 at 70iterations 0.2717064 4.539786 at 80iterations 0.1587504 2.984035 at 90iterations 9.2652239E-02 1.596893 at 100iterations 5.4209802E-02 1.003902 at 110iterations 3.1658091E-02 0.5494690 at 120iterations 1.8552097E-02 0.2974243 at 130iterations 1.0909532E-02 0.1731544 at 140iterations 6.4499392E-03 0.1178017 at 150iterations 3.8549544E-03 6.3457489E-02 at 160iterations 2.3404411E-03 4.3592453E-02 at 170iterations 1.4638057E-03 2.6205063E-02 at 180iterations finished qdiffx linear iterations at : 08:27:06 total time elapsed so far: 21.17000 # loops : 180 mean,max change (kT/e) : 1.4638057E-03 2.6205063E-02 energy calculations done at 21.17000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 21.35000 DelPhi exited at 08:27:07 21.350u 0.475s 0:22.26 98.0% 0+0k 0+0io 0pf+0w