Sat Oct 8 14:50:19 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 Sat Oct 8 2011 at 14:50:19 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3002 !!! WARNING: GLU 313 has a net charge of -0.2720 !!! WARNING: NAP 500 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: 0.6398044 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): -12.23500 43.40700 ymin,ymax (A): -23.96800 22.95500 zmin,zma (A): -7.602000 47.60400 x,y,z range (A): 55.64200 46.92300 55.20600 scale (grids/A): 0.6398044 object centre (A): 15.58600 -0.5065002 20.00100 number of atom coordinates read : 3002 total number of charged atoms : 2857 net assigned charge : 1.728008 assigned positive charge : 449.0646 centred at (gu) : 88.80683 90.00901 91.72687 assigned negative charge : -447.3374 centred at (gu) : 88.73621 89.85629 91.72214 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 8096 nv = 96 ne = 84 npr = 62718 no. pairs analyzed = 62718 no. exposed pairs = 3395 no. arc points = 23986 no. surface atoms = 1159 nbur = 1843 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 400 mr = 4702 m= 0 mr = 46 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3500000 number of dielectric boundary points 3748 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2322 ## 217 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 9885 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4064193E-09 4.6845234E-09 midg,1,midg; midg,igrid,midg -1.8011297E-08 2.2657193E-08 1,midg,midg; igrid,midg,midg -8.9527044E-09 9.2533439E-09 gauss-seidel spectral radius is 0.9873745 estimated iterations to convergence 73 setup time was (sec) 0.6000000 now iterating at: 14:50:20 rms-change max change #iterations 0.1609380 20.05245 at 10iterations 1.5977504E-02 2.315716 at 20iterations 1.6412878E-03 0.2077522 at 30iterations 1.9262453E-04 2.6283264E-02 at 40iterations 2.6595140E-05 4.0206909E-03 at 50iterations finished qdiffx linear iterations at : 14:50:24 total time elapsed so far: 4.400000 # loops : 50 mean,max change (kT/e) : 2.6595140E-05 4.0206909E-03 energy calculations done at 4.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.580000 DelPhi exited at 14:50:24 4.581u 0.402s 0:05.30 93.9% 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 Sat Oct 8 2011 at 14:50:24 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3002 !!! WARNING: GLU 313 has a net charge of -0.2720 !!! WARNING: NAP 500 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: 1.919413 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): -12.23500 43.40700 ymin,ymax (A): -23.96800 22.95500 zmin,zma (A): -7.602000 47.60400 x,y,z range (A): 55.64200 46.92300 55.20600 scale (grids/A): 1.919413 object centre (A): 15.58600 -0.5065002 20.00100 number of atom coordinates read : 3002 total number of charged atoms : 2857 net assigned charge : 1.728008 assigned positive charge : 449.0646 centred at (gu) : 86.41989 90.02649 95.18005 assigned negative charge : -447.3374 centred at (gu) : 86.20855 89.56850 95.16607 start vw surface at 0.1200000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 88911 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23986 grid for indexing accessible points = 1.400000 m= 31887 mr = 64123 m= 4773 mr = 23950 m= 296 mr = 2896 m= 6 mr = 124 m= 0 mr = 0 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 69 time to turn everything in is 0.7000000 number of dielectric boundary points 34780 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 172 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 22519 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) : 0.6398044 object centre at (A) : 15.58600 -0.5065002 20.00100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3147516E-02 1.0340117E-02 midg,1,midg; midg,igrid,midg -1.0814125E-03 3.3420287E-02 1,midg,midg; igrid,midg,midg -2.9678438E-02 1.1335985E-02 gauss-seidel spectral radius is 0.9986890 estimated iterations to convergence 219 setup time was (sec) 0.9900000 now iterating at: 14:50:26 rms-change max change #iterations 4.680172 178.8436 at 10iterations 2.233842 65.91879 at 20iterations 1.062443 33.24099 at 30iterations 0.5059229 15.33255 at 40iterations 0.2404377 6.975341 at 50iterations 0.1148490 3.482533 at 60iterations 5.4758947E-02 1.668325 at 70iterations 2.6017180E-02 0.7787991 at 80iterations 1.2431245E-02 0.3717155 at 90iterations 5.9034871E-03 0.1730717 at 100iterations 2.8095953E-03 8.3963394E-02 at 110iterations 1.3448268E-03 3.8630903E-02 at 120iterations finished qdiffx linear iterations at : 14:50:36 total time elapsed so far: 10.62000 # loops : 120 mean,max change (kT/e) : 1.3448268E-03 3.8630903E-02 energy calculations done at 10.62000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.80000 DelPhi exited at 14:50:36 10.804u 0.445s 0:11.54 97.4% 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 Sat Oct 8 2011 at 14:50:36 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: 284 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3002 !!! WARNING: GLU 313 has a net charge of -0.2720 !!! WARNING: NAP 500 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: 2.879120 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): -12.23500 43.40700 ymin,ymax (A): -23.96800 22.95500 zmin,zma (A): -7.602000 47.60400 x,y,z range (A): 55.64200 46.92300 55.20600 scale (grids/A): 2.879120 object centre (A): 15.58600 -0.5065002 20.00100 number of atom coordinates read : 3002 total number of charged atoms : 2857 net assigned charge : 1.728008 assigned positive charge : 449.0646 centred at (gu) : 84.62971 90.03944 97.76993 assigned negative charge : -447.3374 centred at (gu) : 84.31286 89.35255 97.74895 start vw surface at 0.1400000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 205858 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23986 grid for indexing accessible points = 1.400000 m= 104635 mr = 154591 m= 36385 mr = 87219 m= 8338 mr = 29287 m= 1219 mr = 6181 m= 74 mr = 849 m= 0 mr = 35 time to grow re-entrant surface = 1.140000 no. cavity mid-points inaccessible to solvent = 255 time to turn everything in is 2.200000 number of dielectric boundary points 78347 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.330000 number of grid points assigned charge 22856 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) : 1.919413 object centre at (A) : 15.58600 -0.5065002 20.00100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3462483E-02 0.2596150 midg,1,midg; midg,igrid,midg -8.5288361E-03 0.3585396 1,midg,midg; igrid,midg,midg -0.3042319 0.1725880 gauss-seidel spectral radius is 0.9992782 estimated iterations to convergence 294 setup time was (sec) 2.520000 now iterating at: 14:50:39 rms-change max change #iterations 10.86434 485.3987 at 10iterations 6.361479 139.7978 at 20iterations 3.709870 69.13596 at 30iterations 2.160038 41.02024 at 40iterations 1.252457 24.57249 at 50iterations 0.7283241 11.89800 at 60iterations 0.4220841 7.061523 at 70iterations 0.2447986 4.253684 at 80iterations 0.1417854 2.375877 at 90iterations 8.2213528E-02 1.464722 at 100iterations 4.7569722E-02 0.8057446 at 110iterations 2.7560700E-02 0.4642181 at 120iterations 1.5954535E-02 0.2530384 at 130iterations 9.2456816E-03 0.1548810 at 140iterations 5.3553735E-03 8.6955070E-02 at 150iterations 3.1074523E-03 5.5847168E-02 at 160iterations 1.8074586E-03 3.0293941E-02 at 170iterations 1.0549239E-03 1.9115448E-02 at 180iterations finished qdiffx linear iterations at : 14:50:55 total time elapsed so far: 18.97000 # loops : 180 mean,max change (kT/e) : 1.0549239E-03 1.9115448E-02 energy calculations done at 18.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.14000 DelPhi exited at 14:50:56 19.148u 0.474s 0:19.94 98.3% 0+0k 0+0io 0pf+0w