Tue Oct 11 08:34:24 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 08:34:24 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2044 !!! WARNING: GLM 161 has a net charge of -0.0940 !!! WARNING: SEP 178 has a net charge of -0.4750 !!! WARNING: GLM 180 has a net charge of -0.0940 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: 0.7528496 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): -2.840000 44.44700 ymin,ymax (A): 6.789999 54.02400 zmin,zma (A): -13.52800 29.13200 x,y,z range (A): 47.28700 47.23400 42.66000 scale (grids/A): 0.7528496 object centre (A): 20.80350 30.40700 7.802000 number of atom coordinates read : 2044 total number of charged atoms : 1911 net assigned charge : 6.837009 assigned positive charge : 310.6271 centred at (gu) : 90.70639 91.14255 90.20900 assigned negative charge : -303.7902 centred at (gu) : 90.56316 91.02411 90.25553 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 8092 nv = 96 ne = 84 npr = 40539 no. pairs analyzed = 40539 no. exposed pairs = 2513 no. arc points = 17216 no. surface atoms = 855 nbur = 1189 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 643 mr = 4766 m= 4 mr = 145 m= 0 mr = 0 time to grow re-entrant surface = 8.9999989E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2600000 number of dielectric boundary points 3828 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1435 ## 128 charges are in solution ## iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 8333 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0518445E-07 1.0055742E-07 midg,1,midg; midg,igrid,midg 6.6048234E-09 3.7184316E-07 1,midg,midg; igrid,midg,midg -2.1279783E-08 3.7749035E-07 gauss-seidel spectral radius is 0.9907930 estimated iterations to convergence 85 setup time was (sec) 0.4900000 now iterating at: 08:34:25 rms-change max change #iterations 0.2586719 34.46815 at 10iterations 3.7325293E-02 5.616150 at 20iterations 5.4954016E-03 0.6487007 at 30iterations 9.6331298E-04 0.1151304 at 40iterations 2.4023616E-04 2.7008057E-02 at 50iterations finished qdiffx linear iterations at : 08:34:28 total time elapsed so far: 3.170000 # loops : 50 mean,max change (kT/e) : 2.4023616E-04 2.7008057E-02 energy calculations done at 3.170000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.390000 DelPhi exited at 08:34:28 3.390u 0.210s 0:03.99 90.2% 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 08:34:28 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2044 !!! WARNING: GLM 161 has a net charge of -0.0940 !!! WARNING: SEP 178 has a net charge of -0.4750 !!! WARNING: GLM 180 has a net charge of -0.0940 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: 2.258549 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): -2.840000 44.44700 ymin,ymax (A): 6.789999 54.02400 zmin,zma (A): -13.52800 29.13200 x,y,z range (A): 47.28700 47.23400 42.66000 scale (grids/A): 2.258549 object centre (A): 20.80350 30.40700 7.802000 number of atom coordinates read : 2044 total number of charged atoms : 1911 net assigned charge : 6.837009 assigned positive charge : 310.6271 centred at (gu) : 92.11926 93.42778 90.62718 assigned negative charge : -303.7902 centred at (gu) : 91.68938 93.07240 90.76661 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 84839 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17216 grid for indexing accessible points = 1.400000 m= 37179 mr = 60808 m= 8426 mr = 29027 m= 966 mr = 5958 m= 36 mr = 545 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6300000 number of dielectric boundary points 35108 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 36 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 15222 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) : 0.7528496 object centre at (A) : 20.80350 30.40700 7.802000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5407014E-02 3.2005545E-02 midg,1,midg; midg,igrid,midg -4.2025916E-02 5.2512139E-02 1,midg,midg; igrid,midg,midg 4.8913531E-02 0.1129908 gauss-seidel spectral radius is 0.9989462 estimated iterations to convergence 244 setup time was (sec) 0.9200000 now iterating at: 08:34:30 rms-change max change #iterations 5.088286 180.3816 at 10iterations 2.617536 84.04355 at 20iterations 1.345486 38.37875 at 30iterations 0.6930696 19.67966 at 40iterations 0.3570088 9.946379 at 50iterations 0.1838256 4.938844 at 60iterations 9.4706111E-02 2.608984 at 70iterations 4.8753314E-02 1.367471 at 80iterations 2.5159078E-02 0.6626735 at 90iterations 1.3094255E-02 0.4035950 at 100iterations 6.8395855E-03 0.1828814 at 110iterations 3.6232974E-03 9.5626831E-02 at 120iterations finished qdiffx linear iterations at : 08:34:38 total time elapsed so far: 8.880000 # loops : 120 mean,max change (kT/e) : 3.6232974E-03 9.5626831E-02 energy calculations done at 8.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.050000 DelPhi exited at 08:34:38 9.049u 0.250s 0:09.71 95.6% 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 Tue Oct 11 2011 at 08:34:38 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2044 !!! WARNING: GLM 161 has a net charge of -0.0940 !!! WARNING: SEP 178 has a net charge of -0.4750 !!! WARNING: GLM 180 has a net charge of -0.0940 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: 3.387823 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): -2.840000 44.44700 ymin,ymax (A): 6.789999 54.02400 zmin,zma (A): -13.52800 29.13200 x,y,z range (A): 47.28700 47.23400 42.66000 scale (grids/A): 3.387823 object centre (A): 20.80350 30.40700 7.802000 number of atom coordinates read : 2044 total number of charged atoms : 1911 net assigned charge : 6.837009 assigned positive charge : 310.6271 centred at (gu) : 93.17880 95.14162 90.94078 assigned negative charge : -303.7902 centred at (gu) : 92.53415 94.60863 91.15000 start vw surface at 0.1500000 fill in re-entrant regions at 0.8700000 boundary points on vw surface= 194758 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17216 grid for indexing accessible points = 1.400000 m= 111408 mr = 145629 m= 50699 mr = 93794 m= 16715 mr = 42746 m= 3856 mr = 13466 m= 553 mr = 2907 m= 33 mr = 363 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 1.030000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.030000 number of dielectric boundary points 79115 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.160000 number of grid points assigned charge 15287 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) : 2.258549 object centre at (A) : 20.80350 30.40700 7.802000 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.7782142E-02 0.2460875 midg,1,midg; midg,igrid,midg -0.4882207 0.4473139 1,midg,midg; igrid,midg,midg 0.2911938 0.7225682 gauss-seidel spectral radius is 0.9993281 estimated iterations to convergence 304 setup time was (sec) 2.330000 now iterating at: 08:34:41 rms-change max change #iterations 10.91337 295.4075 at 10iterations 6.569742 173.1769 at 20iterations 3.922971 80.58427 at 30iterations 2.342538 43.93520 at 40iterations 1.396433 27.12304 at 50iterations 0.8297413 15.75190 at 60iterations 0.4938991 8.182587 at 70iterations 0.2944902 5.284386 at 80iterations 0.1748350 2.926573 at 90iterations 0.1035794 1.678754 at 100iterations 6.1694201E-02 1.136974 at 110iterations 3.6969684E-02 0.6062012 at 120iterations 2.2365194E-02 0.3757753 at 130iterations 1.3748119E-02 0.2395020 at 140iterations 8.7136831E-03 0.1551552 at 150iterations 5.7923258E-03 0.1102829 at 160iterations 4.0614153E-03 6.7466736E-02 at 170iterations 3.0249602E-03 5.4924011E-02 at 180iterations finished qdiffx linear iterations at : 08:34:52 total time elapsed so far: 13.14000 # loops : 180 mean,max change (kT/e) : 3.0249602E-03 5.4924011E-02 energy calculations done at 13.14000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.31000 DelPhi exited at 08:34:52 13.313u 0.286s 0:13.99 97.1% 0+0k 0+0io 0pf+0w