Tue Oct 11 08:10:54 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 08:10:54 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1449 !!! WARNING: GLM 67 has a net charge of -0.0940 !!! WARNING: HIZ 68 has a net charge of 0.2000 !!! WARNING: HIZ 159 has a net charge of 0.2000 !!! WARNING: ZN1 185 has a net charge of 1.4000 !!! WARNING: ZN1 186 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6998231 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): -24.40700 26.46300 ymin,ymax (A): -10.05000 31.54000 zmin,zma (A): -33.93300 7.490000 x,y,z range (A): 50.87000 41.59000 41.42300 scale (grids/A): 0.6998231 object centre (A): 1.028000 10.74500 -13.22150 number of atom coordinates read : 1449 total number of charged atoms : 1331 net assigned charge : 3.606004 assigned positive charge : 211.5414 centred at (gu) : 89.23460 90.41705 90.98524 assigned negative charge : -207.9352 centred at (gu) : 89.29571 90.48942 90.90107 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 5011 nv = 96 ne = 84 npr = 27200 no. pairs analyzed = 27200 no. exposed pairs = 2234 no. arc points = 16276 no. surface atoms = 732 nbur = 717 mkacc time = 4.9999997E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 315 mr = 2260 m= 2 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 5.9999995E-02 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.1300000 number of dielectric boundary points 3039 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1329 ## 77 charges are in solution ## iepsmp to db, and charging done at 0.2000000 number of grid points assigned charge 5348 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4833426E-09 5.8473248E-08 midg,1,midg; midg,igrid,midg 4.1456655E-08 5.1182298E-09 1,midg,midg; igrid,midg,midg 4.8634512E-08 7.0546102E-09 gauss-seidel spectral radius is 0.9893146 estimated iterations to convergence 79 setup time was (sec) 0.3200000 now iterating at: 08:10:54 rms-change max change #iterations 0.1594253 28.10840 at 10iterations 1.8420575E-02 3.235027 at 20iterations 2.2026468E-03 0.4194164 at 30iterations 2.5480596E-04 4.3075562E-02 at 40iterations 3.0173607E-05 4.7912598E-03 at 50iterations finished qdiffx linear iterations at : 08:10:57 total time elapsed so far: 3.200000 # loops : 50 mean,max change (kT/e) : 3.0173607E-05 4.7912598E-03 energy calculations done at 3.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.340000 DelPhi exited at 08:10:58 3.345u 0.171s 0:04.52 77.6% 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 08:10:58 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1449 !!! WARNING: GLM 67 has a net charge of -0.0940 !!! WARNING: HIZ 68 has a net charge of 0.2000 !!! WARNING: HIZ 159 has a net charge of 0.2000 !!! WARNING: ZN1 185 has a net charge of 1.4000 !!! WARNING: ZN1 186 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.099469 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): -24.40700 26.46300 ymin,ymax (A): -10.05000 31.54000 zmin,zma (A): -33.93300 7.490000 x,y,z range (A): 50.87000 41.59000 41.42300 scale (grids/A): 2.099469 object centre (A): 1.028000 10.74500 -13.22150 number of atom coordinates read : 1449 total number of charged atoms : 1331 net assigned charge : 3.606004 assigned positive charge : 211.5414 centred at (gu) : 87.70420 91.25131 92.95581 assigned negative charge : -207.9352 centred at (gu) : 87.88724 91.46839 92.70338 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 52493 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16276 grid for indexing accessible points = 1.400000 m= 17764 mr = 32235 m= 3066 mr = 11695 m= 241 mr = 1636 m= 7 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 1257 time to turn everything in is 0.2700000 number of dielectric boundary points 27938 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 0.3600000 number of grid points assigned charge 10566 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) : 0.6998231 object centre at (A) : 1.028000 10.74500 -13.22150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.2913903E-04 2.3423966E-03 midg,1,midg; midg,igrid,midg 2.0748721E-02 -1.2202000E-02 1,midg,midg; igrid,midg,midg 6.7033939E-02 -1.0939619E-02 gauss-seidel spectral radius is 0.9987632 estimated iterations to convergence 225 setup time was (sec) 0.5100000 now iterating at: 08:10:59 rms-change max change #iterations 3.699326 248.7017 at 10iterations 1.779526 79.15199 at 20iterations 0.8637314 33.91486 at 30iterations 0.4158211 15.74349 at 40iterations 0.2010940 7.726307 at 50iterations 9.7325914E-02 3.551116 at 60iterations 4.7022715E-02 1.880282 at 70iterations 2.2738568E-02 0.8412762 at 80iterations 1.0960693E-02 0.3981218 at 90iterations 5.3076823E-03 0.2001972 at 100iterations 2.5687802E-03 0.1068878 at 110iterations 1.2421375E-03 4.7124863E-02 at 120iterations finished qdiffx linear iterations at : 08:11:06 total time elapsed so far: 7.590000 # loops : 120 mean,max change (kT/e) : 1.2421375E-03 4.7124863E-02 energy calculations done at 7.590000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.720000 DelPhi exited at 08:11:07 7.721u 0.253s 0:08.40 94.8% 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 Tue Oct 11 2011 at 08:11:07 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: 285 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1449 !!! WARNING: GLM 67 has a net charge of -0.0940 !!! WARNING: HIZ 68 has a net charge of 0.2000 !!! WARNING: HIZ 159 has a net charge of 0.2000 !!! WARNING: ZN1 185 has a net charge of 1.4000 !!! WARNING: ZN1 186 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.149204 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): -24.40700 26.46300 ymin,ymax (A): -10.05000 31.54000 zmin,zma (A): -33.93300 7.490000 x,y,z range (A): 50.87000 41.59000 41.42300 scale (grids/A): 3.149204 object centre (A): 1.028000 10.74500 -13.22150 number of atom coordinates read : 1449 total number of charged atoms : 1331 net assigned charge : 3.606004 assigned positive charge : 211.5414 centred at (gu) : 86.55617 91.87701 94.43382 assigned negative charge : -207.9352 centred at (gu) : 86.83089 92.20258 94.05511 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 121256 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16276 grid for indexing accessible points = 1.400000 m= 56091 mr = 79252 m= 20428 mr = 42813 m= 5469 mr = 15008 m= 953 mr = 3686 m= 105 mr = 497 m= 5 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.3800000 no. cavity mid-points inaccessible to solvent = 4345 time to turn everything in is 0.7900000 number of dielectric boundary points 62999 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.8700000 number of grid points assigned charge 10647 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) : 2.099469 object centre at (A) : 1.028000 10.74500 -13.22150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3635948E-02 3.3462089E-02 midg,1,midg; midg,igrid,midg 0.2421513 -0.1382751 1,midg,midg; igrid,midg,midg 0.9248901 -0.2033394 gauss-seidel spectral radius is 0.9992980 estimated iterations to convergence 298 setup time was (sec) 1.000000 now iterating at: 08:11:08 rms-change max change #iterations 8.499907 331.3417 at 10iterations 5.066422 135.9863 at 20iterations 2.998686 78.20818 at 30iterations 1.771336 41.93810 at 40iterations 1.040652 23.45079 at 50iterations 0.6100885 13.02757 at 60iterations 0.3572469 8.278780 at 70iterations 0.2087311 4.517520 at 80iterations 0.1217420 2.432060 at 90iterations 7.0999742E-02 1.642504 at 100iterations 4.1347552E-02 0.9073639 at 110iterations 2.4121491E-02 0.5238914 at 120iterations 1.4040930E-02 0.3162689 at 130iterations 8.1780665E-03 0.1661148 at 140iterations 4.7526169E-03 9.9634171E-02 at 150iterations 2.7589668E-03 6.0045242E-02 at 160iterations 1.6130394E-03 3.4904480E-02 at 170iterations 9.3563617E-04 2.0990372E-02 at 180iterations finished qdiffx linear iterations at : 08:11:19 total time elapsed so far: 12.20000 # loops : 180 mean,max change (kT/e) : 9.3563617E-04 2.0990372E-02 energy calculations done at 12.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.34000 DelPhi exited at 08:11:20 12.340u 0.234s 0:13.69 91.8% 0+0k 0+0io 0pf+0w