Tue Oct 11 03:34:02 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 Tue Oct 11 2011 at 03:34:02 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2235 !!! WARNING: ASP 461 has a net charge of -2.0000 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: 0.6442622 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): 22.86000 77.81600 ymin,ymax (A): -5.833000 35.77800 zmin,zma (A): 82.46300 137.7200 x,y,z range (A): 54.95600 41.61100 55.25700 scale (grids/A): 0.6442622 object centre (A): 50.33800 14.97250 110.0915 number of atom coordinates read : 2235 total number of charged atoms : 2129 net assigned charge : -6.499984 assigned positive charge : 328.5384 centred at (gu) : 90.21263 90.23102 90.06820 assigned negative charge : -335.0388 centred at (gu) : 89.99493 90.16507 90.07306 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6208 nv = 96 ne = 84 npr = 46042 no. pairs analyzed = 46042 no. exposed pairs = 2809 no. arc points = 20070 no. surface atoms = 950 nbur = 1285 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 329 mr = 3303 m= 1 mr = 47 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.2900000 number of dielectric boundary points 3188 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1877 ## 142 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 7447 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.0045864E-08 -1.1445732E-08 midg,1,midg; midg,igrid,midg -1.7384686E-08 -3.4719538E-09 1,midg,midg; igrid,midg,midg -3.4353086E-08 1.3968495E-08 gauss-seidel spectral radius is 0.9874876 estimated iterations to convergence 73 setup time was (sec) 0.5100000 now iterating at: 03:34:03 rms-change max change #iterations 0.1389515 24.96062 at 10iterations 1.3535054E-02 2.097092 at 20iterations 1.3619626E-03 0.2230835 at 30iterations 1.3739638E-04 2.0885468E-02 at 40iterations 1.3816783E-05 2.0370483E-03 at 50iterations finished qdiffx linear iterations at : 03:34:06 total time elapsed so far: 2.930000 # loops : 50 mean,max change (kT/e) : 1.3816783E-05 2.0370483E-03 energy calculations done at 2.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 03:34:06 3.109u 0.128s 0:03.79 84.9% 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 03:34:06 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2235 !!! WARNING: ASP 461 has a net charge of -2.0000 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: 1.932787 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): 22.86000 77.81600 ymin,ymax (A): -5.833000 35.77800 zmin,zma (A): 82.46300 137.7200 x,y,z range (A): 54.95600 41.61100 55.25700 scale (grids/A): 1.932787 object centre (A): 50.33800 14.97250 110.0915 number of atom coordinates read : 2235 total number of charged atoms : 2129 net assigned charge : -6.499984 assigned positive charge : 328.5384 centred at (gu) : 90.63757 90.69262 90.20445 assigned negative charge : -335.0388 centred at (gu) : 89.98468 90.49520 90.21921 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 66845 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20070 grid for indexing accessible points = 1.400000 m= 23102 mr = 45558 m= 3656 mr = 16613 m= 208 mr = 2192 m= 8 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 318 time to turn everything in is 0.4900000 number of dielectric boundary points 29415 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 91 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 16765 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) : 0.6442622 object centre at (A) : 50.33800 14.97250 110.0915 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.4771640E-04 -3.6501773E-02 midg,1,midg; midg,igrid,midg 1.2681473E-03 1.3044030E-02 1,midg,midg; igrid,midg,midg -8.3941445E-02 -4.7270376E-02 gauss-seidel spectral radius is 0.9986413 estimated iterations to convergence 215 setup time was (sec) 0.7600000 now iterating at: 03:34:07 rms-change max change #iterations 3.988229 198.8021 at 10iterations 1.868376 72.18449 at 20iterations 0.8762589 32.16523 at 30iterations 0.4095132 14.78645 at 40iterations 0.1922958 6.663250 at 50iterations 8.9868553E-02 2.980969 at 60iterations 4.2073961E-02 1.355061 at 70iterations 1.9781623E-02 0.6903801 at 80iterations 9.2608305E-03 0.2908020 at 90iterations 4.3490520E-03 0.1439095 at 100iterations 2.0417627E-03 8.0207825E-02 at 110iterations 9.5533003E-04 3.1218052E-02 at 120iterations finished qdiffx linear iterations at : 03:34:13 total time elapsed so far: 6.850000 # loops : 120 mean,max change (kT/e) : 9.5533003E-04 3.1218052E-02 energy calculations done at 6.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.040000 DelPhi exited at 03:34:14 7.039u 0.188s 0:07.56 95.3% 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 Tue Oct 11 2011 at 03:34:14 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2235 !!! WARNING: ASP 461 has a net charge of -2.0000 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: 2.899180 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): 22.86000 77.81600 ymin,ymax (A): -5.833000 35.77800 zmin,zma (A): 82.46300 137.7200 x,y,z range (A): 54.95600 41.61100 55.25700 scale (grids/A): 2.899180 object centre (A): 50.33800 14.97250 110.0915 number of atom coordinates read : 2235 total number of charged atoms : 2129 net assigned charge : -6.499984 assigned positive charge : 328.5384 centred at (gu) : 90.95633 91.03883 90.30651 assigned negative charge : -335.0388 centred at (gu) : 89.97704 90.74277 90.32871 start vw surface at 0.1400000 fill in re-entrant regions at 0.4100000 boundary points on vw surface= 154595 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20070 grid for indexing accessible points = 1.400000 m= 74592 mr = 110553 m= 27154 mr = 60111 m= 6533 mr = 21480 m= 892 mr = 4731 m= 54 mr = 567 m= 3 mr = 17 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 1100 time to turn everything in is 1.170000 number of dielectric boundary points 66364 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 17032 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) : 1.932787 object centre at (A) : 50.33800 14.97250 110.0915 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.9235760E-02 -0.4032196 midg,1,midg; midg,igrid,midg 2.7215080E-02 0.1412716 1,midg,midg; igrid,midg,midg -0.9800209 -0.4522043 gauss-seidel spectral radius is 0.9992597 estimated iterations to convergence 290 setup time was (sec) 1.480000 now iterating at: 03:34:16 rms-change max change #iterations 9.300858 339.3143 at 10iterations 5.384902 126.3691 at 20iterations 3.110266 65.22024 at 30iterations 1.786070 36.78397 at 40iterations 1.027089 21.45259 at 50iterations 0.5928074 11.12575 at 60iterations 0.3394191 6.709396 at 70iterations 0.1946628 3.586097 at 80iterations 0.1117026 2.148331 at 90iterations 6.4103015E-02 1.213650 at 100iterations 3.6824305E-02 0.6778803 at 110iterations 2.1125957E-02 0.4321715 at 120iterations 1.2099471E-02 0.2440948 at 130iterations 6.9296686E-03 0.1239800 at 140iterations 3.9796983E-03 7.4928284E-02 at 150iterations 2.2836777E-03 4.5289993E-02 at 160iterations 1.3075556E-03 2.3986816E-02 at 170iterations 7.5125968E-04 1.5197754E-02 at 180iterations finished qdiffx linear iterations at : 03:34:25 total time elapsed so far: 11.20000 # loops : 180 mean,max change (kT/e) : 7.5125968E-04 1.5197754E-02 energy calculations done at 11.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.36000 DelPhi exited at 03:34:26 11.362u 0.239s 0:11.99 96.6% 0+0k 0+0io 0pf+0w