Tue Oct 11 07:29:32 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 07:29:32 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3262 !!! WARNING: HIR 51 has a net charge of 0.5140 !!! WARNING: ILE 264 has a net charge of -0.5000 !!! WARNING: UMP 529 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5934718 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): 0.8519999 50.26600 ymin,ymax (A): -8.035000 49.00200 zmin,zma (A): 0.9969999 60.98300 x,y,z range (A): 49.41400 57.03700 59.98600 scale (grids/A): 0.5934718 object centre (A): 25.55900 20.48350 30.99000 number of atom coordinates read : 3262 total number of charged atoms : 3110 net assigned charge : 0.4140097 assigned positive charge : 492.7567 centred at (gu) : 89.22935 89.45218 90.79406 assigned negative charge : -492.3439 centred at (gu) : 89.16452 89.36905 90.72930 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 7586 nv = 96 ne = 84 npr = 67109 no. pairs analyzed = 67109 no. exposed pairs = 3857 no. arc points = 25732 no. surface atoms = 1321 nbur = 1941 mkacc time = 0.1200000 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 = 1.456000 m= 362 mr = 4380 m= 1 mr = 36 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3533 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2629 ## 255 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 9522 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9064748E-09 3.1145091E-09 midg,1,midg; midg,igrid,midg -3.4110621E-09 2.8767468E-09 1,midg,midg; igrid,midg,midg -2.7547287E-09 2.1657278E-09 gauss-seidel spectral radius is 0.9853557 estimated iterations to convergence 68 setup time was (sec) 0.4300000 now iterating at: 07:29:33 rms-change max change #iterations 0.1190033 17.47840 at 10iterations 1.1069370E-02 1.791672 at 20iterations 1.4451437E-03 0.2107029 at 30iterations 3.6134699E-04 5.8376312E-02 at 40iterations 1.0643655E-04 1.7019272E-02 at 50iterations finished qdiffx linear iterations at : 07:29:36 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 1.0643655E-04 1.7019272E-02 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.460000 DelPhi exited at 07:29:36 3.468u 0.165s 0:03.92 92.3% 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 07:29:36 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3262 !!! WARNING: HIR 51 has a net charge of 0.5140 !!! WARNING: ILE 264 has a net charge of -0.5000 !!! WARNING: UMP 529 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.780416 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): 0.8519999 50.26600 ymin,ymax (A): -8.035000 49.00200 zmin,zma (A): 0.9969999 60.98300 x,y,z range (A): 49.41400 57.03700 59.98600 scale (grids/A): 1.780416 object centre (A): 25.55900 20.48350 30.99000 number of atom coordinates read : 3262 total number of charged atoms : 3110 net assigned charge : 0.4140097 assigned positive charge : 492.7567 centred at (gu) : 87.68732 88.35570 92.38100 assigned negative charge : -492.3439 centred at (gu) : 87.49331 88.10693 92.18751 start vw surface at 0.1100000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 82891 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25732 grid for indexing accessible points = 1.400000 m= 30312 mr = 59737 m= 4112 mr = 22910 m= 147 mr = 2496 m= 0 mr = 33 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 766 time to turn everything in is 0.4100000 number of dielectric boundary points 32286 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 209 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 24256 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) : 0.5934718 object centre at (A) : 25.55900 20.48350 30.99000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4205378E-02 1.1904413E-02 midg,1,midg; midg,igrid,midg -1.8446235E-02 8.5239122E-03 1,midg,midg; igrid,midg,midg 5.8045583E-03 1.3716060E-02 gauss-seidel spectral radius is 0.9985020 estimated iterations to convergence 205 setup time was (sec) 0.6200000 now iterating at: 07:29:37 rms-change max change #iterations 4.267903 193.1961 at 10iterations 1.929779 64.24591 at 20iterations 0.8758530 26.79545 at 30iterations 0.3937978 12.26779 at 40iterations 0.1788927 5.509357 at 50iterations 8.1570715E-02 2.492094 at 60iterations 3.7064202E-02 1.268265 at 70iterations 1.6891310E-02 0.5014877 at 80iterations 7.7964296E-03 0.2350354 at 90iterations 3.6970775E-03 0.1168404 at 100iterations 1.7934549E-03 6.1374664E-02 at 110iterations 9.0868509E-04 3.4049034E-02 at 120iterations finished qdiffx linear iterations at : 07:29:44 total time elapsed so far: 7.810000 # loops : 120 mean,max change (kT/e) : 9.0868509E-04 3.4049034E-02 energy calculations done at 7.810000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.940000 DelPhi exited at 07:29:45 7.941u 0.207s 0:08.84 92.0% 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 07:29:45 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: 313 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3262 !!! WARNING: HIR 51 has a net charge of 0.5140 !!! WARNING: ILE 264 has a net charge of -0.5000 !!! WARNING: UMP 529 has a net charge of -0.1000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.670623 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): 0.8519999 50.26600 ymin,ymax (A): -8.035000 49.00200 zmin,zma (A): 0.9969999 60.98300 x,y,z range (A): 49.41400 57.03700 59.98600 scale (grids/A): 2.670623 object centre (A): 25.55900 20.48350 30.99000 number of atom coordinates read : 3262 total number of charged atoms : 3110 net assigned charge : 0.4140097 assigned positive charge : 492.7567 centred at (gu) : 86.53056 87.53319 93.57133 assigned negative charge : -492.3439 centred at (gu) : 86.23987 87.16023 93.28116 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 192031 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25732 grid for indexing accessible points = 1.400000 m= 99874 mr = 144489 m= 34343 mr = 83077 m= 6987 mr = 27998 m= 613 mr = 5196 m= 15 mr = 340 m= 0 mr = 3 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 2447 time to turn everything in is 1.040000 number of dielectric boundary points 72760 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.140000 number of grid points assigned charge 24870 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) : 1.780416 object centre at (A) : 25.55900 20.48350 30.99000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.3522704 0.1112391 midg,1,midg; midg,igrid,midg -0.3538784 0.1171521 1,midg,midg; igrid,midg,midg 0.1558692 0.1620917 gauss-seidel spectral radius is 0.9992307 estimated iterations to convergence 285 setup time was (sec) 1.280000 now iterating at: 07:29:47 rms-change max change #iterations 10.31283 284.9012 at 10iterations 5.980785 129.3843 at 20iterations 3.440627 71.67923 at 30iterations 1.971676 34.67353 at 40iterations 1.128485 19.98124 at 50iterations 0.6460385 12.19942 at 60iterations 0.3696207 6.534298 at 70iterations 0.2108994 3.912895 at 80iterations 0.1203870 2.045723 at 90iterations 6.8549626E-02 1.290337 at 100iterations 3.9075956E-02 0.6779022 at 110iterations 2.2269949E-02 0.3962579 at 120iterations 1.2721823E-02 0.2186890 at 130iterations 7.3111793E-03 0.1292610 at 140iterations 4.2268033E-03 8.5901260E-02 at 150iterations 2.4804352E-03 4.4902802E-02 at 160iterations 1.4849645E-03 2.8995514E-02 at 170iterations 9.1981923E-04 1.6979218E-02 at 180iterations finished qdiffx linear iterations at : 07:29:58 total time elapsed so far: 12.88000 # loops : 180 mean,max change (kT/e) : 9.1981923E-04 1.6979218E-02 energy calculations done at 12.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.01000 DelPhi exited at 07:29:59 13.008u 0.232s 0:13.80 95.8% 0+0k 0+0io 0pf+0w