Sun Oct 9 07:50:55 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 Sun Oct 9 2011 at 07:50:55 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2211 !!! WARNING: NAP 207 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7096581 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): -15.84000 30.74000 ymin,ymax (A): -19.92300 30.24200 zmin,zma (A): -5.093000 35.55600 x,y,z range (A): 46.58000 50.16500 40.64900 scale (grids/A): 0.7096581 object centre (A): 7.450000 5.159499 15.23150 number of atom coordinates read : 2211 total number of charged atoms : 2074 net assigned charge : 6.000020 assigned positive charge : 333.8635 centred at (gu) : 89.78327 90.65585 90.67042 assigned negative charge : -327.8639 centred at (gu) : 89.66798 90.75234 90.80045 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7485 nv = 96 ne = 84 npr = 45988 no. pairs analyzed = 45988 no. exposed pairs = 2698 no. arc points = 19108 no. surface atoms = 912 nbur = 1299 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 489 mr = 4230 m= 1 mr = 103 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 193 time to turn everything in is 0.3200000 number of dielectric boundary points 3642 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1813 ## 177 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8418 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0937974E-07 -2.0334619E-08 midg,1,midg; midg,igrid,midg 9.3981100E-08 1.0716549E-09 1,midg,midg; igrid,midg,midg -9.6574002E-09 1.1187235E-07 gauss-seidel spectral radius is 0.9896647 estimated iterations to convergence 80 setup time was (sec) 0.5900000 now iterating at: 07:50:56 rms-change max change #iterations 0.2156247 30.36374 at 10iterations 2.6530636E-02 3.528191 at 20iterations 3.2884111E-03 0.4018669 at 30iterations 4.1432155E-04 6.4743042E-02 at 40iterations 4.9859096E-05 6.0033798E-03 at 50iterations finished qdiffx linear iterations at : 07:50:59 total time elapsed so far: 3.850000 # loops : 50 mean,max change (kT/e) : 4.9859096E-05 6.0033798E-03 energy calculations done at 3.850000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.030000 DelPhi exited at 07:51:00 4.029u 0.249s 0:04.55 93.6% 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 Sun Oct 9 2011 at 07:51:00 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2211 !!! WARNING: NAP 207 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.128974 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): -15.84000 30.74000 ymin,ymax (A): -19.92300 30.24200 zmin,zma (A): -5.093000 35.55600 x,y,z range (A): 46.58000 50.16500 40.64900 scale (grids/A): 2.128974 object centre (A): 7.450000 5.159499 15.23150 number of atom coordinates read : 2211 total number of charged atoms : 2074 net assigned charge : 6.000020 assigned positive charge : 333.8635 centred at (gu) : 89.34920 91.96748 92.01089 assigned negative charge : -327.8639 centred at (gu) : 89.00394 92.25706 92.40130 start vw surface at 0.1400000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 78281 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19108 grid for indexing accessible points = 1.400000 m= 31896 mr = 54078 m= 6695 mr = 24717 m= 679 mr = 4713 m= 27 mr = 379 m= 0 mr = 13 time to grow re-entrant surface = 0.3700000 no. cavity mid-points inaccessible to solvent = 4656 time to turn everything in is 0.7100000 number of dielectric boundary points 33678 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 85 iepsmp to db, and charging done at 0.8500000 number of grid points assigned charge 16484 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) : 0.7096581 object centre at (A) : 7.450000 5.159499 15.23150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.8776496E-02 2.2129780E-02 midg,1,midg; midg,igrid,midg 4.9253542E-02 1.1990375E-03 1,midg,midg; igrid,midg,midg -1.6663706E-02 3.1150674E-02 gauss-seidel spectral radius is 0.9988521 estimated iterations to convergence 234 setup time was (sec) 1.010000 now iterating at: 07:51:01 rms-change max change #iterations 4.863187 201.8101 at 10iterations 2.416019 80.09523 at 20iterations 1.202049 36.71811 at 30iterations 0.6001955 17.72083 at 40iterations 0.2988486 9.764082 at 50iterations 0.1488479 5.677608 at 60iterations 7.4473746E-02 2.089163 at 70iterations 3.7138849E-02 1.166109 at 80iterations 1.8501543E-02 0.5677679 at 90iterations 9.2064925E-03 0.2568398 at 100iterations 4.5956182E-03 0.1401672 at 110iterations 2.2959819E-03 6.9491863E-02 at 120iterations finished qdiffx linear iterations at : 07:51:09 total time elapsed so far: 9.310000 # loops : 120 mean,max change (kT/e) : 2.2959819E-03 6.9491863E-02 energy calculations done at 9.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.490000 DelPhi exited at 07:51:10 9.494u 0.297s 0:10.09 96.9% 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 Sun Oct 9 2011 at 07:51:10 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: 309 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2211 !!! WARNING: NAP 207 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.193461 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): -15.84000 30.74000 ymin,ymax (A): -19.92300 30.24200 zmin,zma (A): -5.093000 35.55600 x,y,z range (A): 46.58000 50.16500 40.64900 scale (grids/A): 3.193461 object centre (A): 7.450000 5.159499 15.23150 number of atom coordinates read : 2211 total number of charged atoms : 2074 net assigned charge : 6.000020 assigned positive charge : 333.8635 centred at (gu) : 89.02374 92.95115 93.01612 assigned negative charge : -327.8639 centred at (gu) : 88.50584 93.38559 93.60194 start vw surface at 0.1600000 fill in re-entrant regions at 1.070000 boundary points on vw surface= 180032 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19108 grid for indexing accessible points = 1.400000 m= 97305 mr = 129984 m= 42491 mr = 81612 m= 12821 mr = 35584 m= 2728 mr = 10289 m= 402 mr = 2096 m= 26 mr = 313 m= 0 mr = 15 time to grow re-entrant surface = 1.160000 no. cavity mid-points inaccessible to solvent = 15877 time to turn everything in is 2.350000 number of dielectric boundary points 75912 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.510000 number of grid points assigned charge 16592 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) : 2.128974 object centre at (A) : 7.450000 5.159499 15.23150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.6212887 0.1847484 midg,1,midg; midg,igrid,midg 0.4295241 0.1736978 1,midg,midg; igrid,midg,midg -9.4262064E-02 0.2014513 gauss-seidel spectral radius is 0.9992952 estimated iterations to convergence 297 setup time was (sec) 2.680000 now iterating at: 07:51:13 rms-change max change #iterations 10.64934 440.5837 at 10iterations 6.191764 135.7827 at 20iterations 3.603290 66.67721 at 30iterations 2.099145 37.02142 at 40iterations 1.223319 21.01240 at 50iterations 0.7116998 12.82463 at 60iterations 0.4141859 7.861133 at 70iterations 0.2406270 4.122589 at 80iterations 0.1400051 2.376057 at 90iterations 8.1266977E-02 1.329704 at 100iterations 4.7269847E-02 0.8657103 at 110iterations 2.7443295E-02 0.4421034 at 120iterations 1.5988821E-02 0.2650928 at 130iterations 9.3062017E-03 0.1555729 at 140iterations 5.4058195E-03 8.5601807E-02 at 150iterations 3.1497884E-03 5.5085182E-02 at 160iterations 1.8312928E-03 3.1623840E-02 at 170iterations 1.0667102E-03 1.8422604E-02 at 180iterations finished qdiffx linear iterations at : 07:51:26 total time elapsed so far: 16.37000 # loops : 180 mean,max change (kT/e) : 1.0667102E-03 1.8422604E-02 energy calculations done at 16.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.55000 DelPhi exited at 07:51:27 16.552u 0.292s 0:17.13 98.3% 0+0k 0+0io 0pf+0w