Sun Oct 9 20:56:00 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 20:56:00 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2499 !!! WARNING: SEP 158 has a net charge of -0.4750 !!! WARNING: CYS 277 has a net charge of 0.5000 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: 0.6299101 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): -40.02100 16.49500 ymin,ymax (A): -11.99500 32.19500 zmin,zma (A): -17.16900 36.47400 x,y,z range (A): 56.51600 44.19000 53.64300 scale (grids/A): 0.6299101 object centre (A): -11.76300 10.10000 9.652499 number of atom coordinates read : 2499 total number of charged atoms : 2354 net assigned charge : 4.525007 assigned positive charge : 376.9690 centred at (gu) : 91.48129 88.93578 90.04345 assigned negative charge : -372.4446 centred at (gu) : 91.55858 88.89317 89.97687 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6517 nv = 96 ne = 84 npr = 50949 no. pairs analyzed = 50949 no. exposed pairs = 3099 no. arc points = 22030 no. surface atoms = 1054 nbur = 1445 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 368 mr = 3491 m= 5 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 63 time to turn everything in is 0.3000000 number of dielectric boundary points 3355 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2268 ## 248 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 8062 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.0393218E-10 1.0720519E-08 midg,1,midg; midg,igrid,midg 1.7385707E-09 6.8722557E-09 1,midg,midg; igrid,midg,midg 8.3777651E-09 -2.2517106E-09 gauss-seidel spectral radius is 0.9869373 estimated iterations to convergence 72 setup time was (sec) 0.5400000 now iterating at: 20:56:01 rms-change max change #iterations 0.1341883 23.25491 at 10iterations 1.2807476E-02 1.811689 at 20iterations 1.2144203E-03 0.1949048 at 30iterations 1.1676751E-04 1.6160965E-02 at 40iterations 1.1039667E-05 1.5702248E-03 at 50iterations finished qdiffx linear iterations at : 20:56:03 total time elapsed so far: 3.130000 # loops : 50 mean,max change (kT/e) : 1.1039667E-05 1.5702248E-03 energy calculations done at 3.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 20:56:04 3.317u 0.151s 0:03.74 92.5% 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 20:56:04 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2499 !!! WARNING: SEP 158 has a net charge of -0.4750 !!! WARNING: CYS 277 has a net charge of 0.5000 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: 1.889730 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): -40.02100 16.49500 ymin,ymax (A): -11.99500 32.19500 zmin,zma (A): -17.16900 36.47400 x,y,z range (A): 56.51600 44.19000 53.64300 scale (grids/A): 1.889730 object centre (A): -11.76300 10.10000 9.652499 number of atom coordinates read : 2499 total number of charged atoms : 2354 net assigned charge : 4.525007 assigned positive charge : 376.9690 centred at (gu) : 94.44337 86.80672 90.12965 assigned negative charge : -372.4446 centred at (gu) : 94.67542 86.67943 89.93044 start vw surface at 0.1600000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 70338 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22030 grid for indexing accessible points = 1.400000 m= 23590 mr = 47667 m= 3741 mr = 16868 m= 274 mr = 2308 m= 2 mr = 118 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1697 time to turn everything in is 0.5300000 number of dielectric boundary points 30984 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 172 iepsmp to db, and charging done at 0.6500000 number of grid points assigned charge 18483 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) : 0.6299101 object centre at (A) : -11.76300 10.10000 9.652499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.4665725E-02 2.1511901E-02 midg,1,midg; midg,igrid,midg -1.5569355E-02 -1.4843394E-03 1,midg,midg; igrid,midg,midg 4.3632649E-02 -2.2080343E-03 gauss-seidel spectral radius is 0.9985983 estimated iterations to convergence 212 setup time was (sec) 0.8200000 now iterating at: 20:56:05 rms-change max change #iterations 4.066103 175.4192 at 10iterations 1.873685 67.80940 at 20iterations 0.8695368 29.11862 at 30iterations 0.4024738 12.20486 at 40iterations 0.1862123 7.014441 at 50iterations 8.6372502E-02 2.971273 at 60iterations 3.9868664E-02 1.395988 at 70iterations 1.8523213E-02 0.6095982 at 80iterations 8.5633565E-03 0.3234034 at 90iterations 3.9716018E-03 0.1238594 at 100iterations 1.8347866E-03 6.1714172E-02 at 110iterations 8.5276819E-04 2.7347088E-02 at 120iterations finished qdiffx linear iterations at : 20:56:11 total time elapsed so far: 7.410000 # loops : 120 mean,max change (kT/e) : 8.5276819E-04 2.7347088E-02 energy calculations done at 7.410000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.610000 DelPhi exited at 20:56:12 7.611u 0.159s 0:08.08 96.0% 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 20:56:12 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: 264 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2499 !!! WARNING: SEP 158 has a net charge of -0.4750 !!! WARNING: CYS 277 has a net charge of 0.5000 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: 2.834596 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): -40.02100 16.49500 ymin,ymax (A): -11.99500 32.19500 zmin,zma (A): -17.16900 36.47400 x,y,z range (A): 56.51600 44.19000 53.64300 scale (grids/A): 2.834596 object centre (A): -11.76300 10.10000 9.652499 number of atom coordinates read : 2499 total number of charged atoms : 2354 net assigned charge : 4.525007 assigned positive charge : 376.9690 centred at (gu) : 96.66502 85.20994 90.19431 assigned negative charge : -372.4446 centred at (gu) : 97.01317 85.01916 89.89553 start vw surface at 0.1500000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 162924 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22030 grid for indexing accessible points = 1.400000 m= 77508 mr = 115892 m= 26659 mr = 62328 m= 6641 mr = 20997 m= 1194 mr = 4998 m= 87 mr = 853 m= 0 mr = 37 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 5528 time to turn everything in is 1.290000 number of dielectric boundary points 69908 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.430000 number of grid points assigned charge 18830 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) : 1.889730 object centre at (A) : -11.76300 10.10000 9.652499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2416347 0.1999181 midg,1,midg; midg,igrid,midg -0.1275847 -4.1875638E-02 1,midg,midg; igrid,midg,midg 0.4723693 -0.1332556 gauss-seidel spectral radius is 0.9992468 estimated iterations to convergence 288 setup time was (sec) 1.600000 now iterating at: 20:56:14 rms-change max change #iterations 9.528532 339.4617 at 10iterations 5.495697 121.5174 at 20iterations 3.151974 60.28761 at 30iterations 1.802780 38.31950 at 40iterations 1.030476 18.99565 at 50iterations 0.5894029 11.90580 at 60iterations 0.3370598 6.246724 at 70iterations 0.1921529 3.418598 at 80iterations 0.1097302 2.114594 at 90iterations 6.2529400E-02 1.139391 at 100iterations 3.5780005E-02 0.6615429 at 110iterations 2.0382132E-02 0.4022329 at 120iterations 1.1635067E-02 0.2438278 at 130iterations 6.6517140E-03 0.1263669 at 140iterations 3.7948780E-03 7.1673393E-02 at 150iterations 2.1615212E-03 4.0037632E-02 at 160iterations 1.2346290E-03 2.2425175E-02 at 170iterations 7.0619938E-04 1.2376785E-02 at 180iterations finished qdiffx linear iterations at : 20:56:24 total time elapsed so far: 11.72000 # loops : 180 mean,max change (kT/e) : 7.0619938E-04 1.2376785E-02 energy calculations done at 11.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.91000 DelPhi exited at 20:56:24 11.918u 0.169s 0:12.36 97.6% 0+0k 0+0io 0pf+0w