Sun Oct 9 22:05:03 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 Sun Oct 9 2011 at 22:05:03 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2564 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: GLM 163 has a net charge of -0.6000 !!! WARNING: ZN6 634 has a net charge of 1.4000 !!! WARNING: ZN6 635 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6336662 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): 17.22000 73.40100 ymin,ymax (A): -14.33500 37.59000 zmin,zma (A): -2.169000 49.50300 x,y,z range (A): 56.18100 51.92500 51.67200 scale (grids/A): 0.6336662 object centre (A): 45.31050 11.62750 23.66700 number of atom coordinates read : 2564 total number of charged atoms : 2434 net assigned charge : 8.300010 assigned positive charge : 391.2979 centred at (gu) : 90.89229 90.96667 90.22478 assigned negative charge : -382.9987 centred at (gu) : 90.92844 90.88271 90.25873 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6648 nv = 96 ne = 84 npr = 52148 no. pairs analyzed = 52148 no. exposed pairs = 3172 no. arc points = 22435 no. surface atoms = 1064 nbur = 1500 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 342 mr = 3561 m= 2 mr = 25 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 18 time to turn everything in is 0.2900000 number of dielectric boundary points 3406 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2194 ## 226 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8242 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2651739E-08 7.0214652E-09 midg,1,midg; midg,igrid,midg 1.5626286E-09 2.2198083E-08 1,midg,midg; igrid,midg,midg 1.1171585E-08 7.7831110E-09 gauss-seidel spectral radius is 0.9870926 estimated iterations to convergence 72 setup time was (sec) 0.5200000 now iterating at: 22:05:04 rms-change max change #iterations 0.1433562 27.30396 at 10iterations 1.3730658E-02 2.392029 at 20iterations 1.3210702E-03 0.2103329 at 30iterations 1.2823440E-04 1.7498970E-02 at 40iterations 1.2564878E-05 1.7204285E-03 at 50iterations finished qdiffx linear iterations at : 22:05:06 total time elapsed so far: 3.150000 # loops : 50 mean,max change (kT/e) : 1.2564878E-05 1.7204285E-03 energy calculations done at 3.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 22:05:07 3.329u 0.214s 0:03.92 90.0% 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 Sun Oct 9 2011 at 22:05:07 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2564 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: GLM 163 has a net charge of -0.6000 !!! WARNING: ZN6 634 has a net charge of 1.4000 !!! WARNING: ZN6 635 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.900999 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): 17.22000 73.40100 ymin,ymax (A): -14.33500 37.59000 zmin,zma (A): -2.169000 49.50300 x,y,z range (A): 56.18100 51.92500 51.67200 scale (grids/A): 1.900999 object centre (A): 45.31050 11.62750 23.66700 number of atom coordinates read : 2564 total number of charged atoms : 2434 net assigned charge : 8.300010 assigned positive charge : 391.2979 centred at (gu) : 92.67653 92.89896 90.67334 assigned negative charge : -382.9987 centred at (gu) : 92.78515 92.64790 90.77601 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 72494 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22435 grid for indexing accessible points = 1.400000 m= 24091 mr = 49420 m= 3603 mr = 17312 m= 219 mr = 2093 m= 4 mr = 88 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 970 time to turn everything in is 0.5000000 number of dielectric boundary points 31498 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 143 iepsmp to db, and charging done at 0.6200000 number of grid points assigned charge 19108 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) : 0.6336662 object centre at (A) : 45.31050 11.62750 23.66700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0613452E-02 -8.8418089E-03 midg,1,midg; midg,igrid,midg 1.6184632E-03 4.4941191E-02 1,midg,midg; igrid,midg,midg -3.7856982E-03 3.1678975E-02 gauss-seidel spectral radius is 0.9986199 estimated iterations to convergence 213 setup time was (sec) 0.7900000 now iterating at: 22:05:08 rms-change max change #iterations 4.199856 171.2408 at 10iterations 1.947369 77.21086 at 20iterations 0.9097489 28.83183 at 30iterations 0.4230319 13.16362 at 40iterations 0.1969107 6.196604 at 50iterations 9.1985226E-02 3.019060 at 60iterations 4.2759493E-02 1.460247 at 70iterations 1.9982366E-02 0.6122742 at 80iterations 9.3266172E-03 0.2927380 at 90iterations 4.3455386E-03 0.1402054 at 100iterations 2.0262210E-03 6.2898636E-02 at 110iterations 9.4485196E-04 2.9967308E-02 at 120iterations finished qdiffx linear iterations at : 22:05:15 total time elapsed so far: 7.450000 # loops : 120 mean,max change (kT/e) : 9.4485196E-04 2.9967308E-02 energy calculations done at 7.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.610000 DelPhi exited at 22:05:15 7.613u 0.242s 0:08.23 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 Sun Oct 9 2011 at 22:05:15 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2564 !!! WARNING: GLM 39 has a net charge of -0.6000 !!! WARNING: HIZ 43 has a net charge of 0.2000 !!! WARNING: GLM 163 has a net charge of -0.6000 !!! WARNING: ZN6 634 has a net charge of 1.4000 !!! WARNING: ZN6 635 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.851498 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): 17.22000 73.40100 ymin,ymax (A): -14.33500 37.59000 zmin,zma (A): -2.169000 49.50300 x,y,z range (A): 56.18100 51.92500 51.67200 scale (grids/A): 2.851498 object centre (A): 45.31050 11.62750 23.66700 number of atom coordinates read : 2564 total number of charged atoms : 2434 net assigned charge : 8.300010 assigned positive charge : 391.2979 centred at (gu) : 94.01443 94.34839 91.01001 assigned negative charge : -382.9987 centred at (gu) : 94.17771 93.97189 91.16400 start vw surface at 0.1300000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 167797 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22435 grid for indexing accessible points = 1.400000 m= 80313 mr = 120279 m= 27087 mr = 64881 m= 6187 mr = 20995 m= 894 mr = 4445 m= 72 mr = 617 m= 0 mr = 46 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 3205 time to turn everything in is 1.260000 number of dielectric boundary points 71087 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.400000 number of grid points assigned charge 19470 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) : 1.900999 object centre at (A) : 45.31050 11.62750 23.66700 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2590996 -0.2470695 midg,1,midg; midg,igrid,midg -0.1897744 0.5711247 1,midg,midg; igrid,midg,midg 1.0674518E-02 0.2883863 gauss-seidel spectral radius is 0.9992554 estimated iterations to convergence 289 setup time was (sec) 1.570000 now iterating at: 22:05:17 rms-change max change #iterations 9.881173 372.4743 at 10iterations 5.777693 128.2487 at 20iterations 3.340846 67.42114 at 30iterations 1.929588 41.16715 at 40iterations 1.111712 21.69383 at 50iterations 0.6403366 12.82801 at 60iterations 0.3682386 6.546912 at 70iterations 0.2114751 4.014343 at 80iterations 0.1212922 2.331167 at 90iterations 6.9778882E-02 1.339005 at 100iterations 3.9994475E-02 0.7797890 at 110iterations 2.2949828E-02 0.4269848 at 120iterations 1.3155466E-02 0.2371035 at 130iterations 7.5466111E-03 0.1380281 at 140iterations 4.3163877E-03 7.3242188E-02 at 150iterations 2.4798976E-03 4.3538332E-02 at 160iterations 1.4213779E-03 2.5840759E-02 at 170iterations 8.1760995E-04 1.7833710E-02 at 180iterations finished qdiffx linear iterations at : 22:05:27 total time elapsed so far: 11.83000 # loops : 180 mean,max change (kT/e) : 8.1760995E-04 1.7833710E-02 energy calculations done at 11.83000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.99000 DelPhi exited at 22:05:28 11.992u 0.265s 0:12.68 96.6% 0+0k 0+0io 0pf+0w