Thu Dec 22 14:23:26 PST 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 Thu Dec 22 2011 at 14:23:26 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5568504 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): -9.924999 35.30200 ymin,ymax (A): 0.4000000 42.02600 zmin,zma (A): -17.94900 45.98200 x,y,z range (A): 45.22700 41.62600 63.93100 scale (grids/A): 0.5568504 object centre (A): 12.68850 21.21300 14.01650 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000006 assigned positive charge : 289.0260 centred at (gu) : 89.55137 89.65448 89.99413 assigned negative charge : -287.0263 centred at (gu) : 89.64159 89.81516 89.99719 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 4123 nv = 96 ne = 84 npr = 40041 no. pairs analyzed = 40041 no. exposed pairs = 2434 no. arc points = 17008 no. surface atoms = 835 nbur = 1129 mkacc time = 8.0000006E-02 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 = 1.568000 m= 173 mr = 2202 m= 0 mr = 16 time to grow re-entrant surface = 8.9999996E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 2078 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1810 ## 244 charges are in solution ## iepsmp to db, and charging done at 0.2700000 number of grid points assigned charge 5210 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.0330861E-10 1.6356251E-10 midg,1,midg; midg,igrid,midg 1.2967740E-09 -7.9366164E-10 1,midg,midg; igrid,midg,midg 8.4186624E-10 -3.5740724E-10 gauss-seidel spectral radius is 0.9832872 estimated iterations to convergence 64 setup time was (sec) 0.4000000 now iterating at: 14:23:27 rms-change max change #iterations 6.5484837E-02 11.69331 at 10iterations 4.6489360E-03 0.9120989 at 20iterations 3.1753434E-04 6.2057495E-02 at 30iterations 2.2710716E-05 5.3329468E-03 at 40iterations 1.5600007E-06 2.8610229E-04 at 50iterations finished qdiffx linear iterations at : 14:23:30 total time elapsed so far: 3.350000 # loops : 50 mean,max change (kT/e) : 1.5600007E-06 2.8610229E-04 energy calculations done at 3.350000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.490000 DelPhi exited at 14:23:30 3.496u 0.189s 0:04.00 91.7% 0+0k 0+45552io 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 Thu Dec 22 2011 at 14:23:30 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.670551 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): -9.924999 35.30200 ymin,ymax (A): 0.4000000 42.02600 zmin,zma (A): -17.94900 45.98200 x,y,z range (A): 45.22700 41.62600 63.93100 scale (grids/A): 1.670551 object centre (A): 12.68850 21.21300 14.01650 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000006 assigned positive charge : 289.0260 centred at (gu) : 88.65429 88.96359 89.98244 assigned negative charge : -287.0263 centred at (gu) : 88.92503 89.44559 89.99168 start vw surface at 0.1000000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 44818 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17008 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 15224 mr = 30411 m= 1778 mr = 11260 m= 56 mr = 987 m= 0 mr = 5 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 259 time to turn everything in is 0.3000000 number of dielectric boundary points 19213 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 251 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 14121 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) : 0.5568504 object centre at (A) : 12.68850 21.21300 14.01650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2524497E-02 1.2235647E-02 midg,1,midg; midg,igrid,midg 2.4921419E-03 -5.6260894E-03 1,midg,midg; igrid,midg,midg -1.1358229E-03 -1.9425728E-03 gauss-seidel spectral radius is 0.9981472 estimated iterations to convergence 185 setup time was (sec) 0.5100000 now iterating at: 14:23:31 rms-change max change #iterations 2.750499 144.2959 at 10iterations 1.129892 51.97058 at 20iterations 0.4681638 24.12005 at 30iterations 0.1928427 8.847061 at 40iterations 8.0049671E-02 3.517445 at 50iterations 3.2913987E-02 1.369038 at 60iterations 1.3612550E-02 0.5570297 at 70iterations 5.6232749E-03 0.2587662 at 80iterations 2.3287146E-03 0.1003437 at 90iterations 9.5826725E-04 4.5318604E-02 at 100iterations 3.9766653E-04 1.6426086E-02 at 110iterations 1.6421774E-04 7.4996948E-03 at 120iterations finished qdiffx linear iterations at : 14:23:38 total time elapsed so far: 7.610000 # loops : 120 mean,max change (kT/e) : 1.6421774E-04 7.4996948E-03 energy calculations done at 7.610000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.750000 DelPhi exited at 14:23:39 7.754u 0.200s 0:08.30 95.7% 0+0k 0+45144io 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 Thu Dec 22 2011 at 14:23:39 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: 250 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.505827 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): -9.924999 35.30200 ymin,ymax (A): 0.4000000 42.02600 zmin,zma (A): -17.94900 45.98200 x,y,z range (A): 45.22700 41.62600 63.93100 scale (grids/A): 2.505827 object centre (A): 12.68850 21.21300 14.01650 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 2.000006 assigned positive charge : 289.0260 centred at (gu) : 87.98132 88.44547 89.97367 assigned negative charge : -287.0263 centred at (gu) : 88.38768 89.16840 89.98745 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 103608 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17008 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 50859 mr = 73817 m= 16552 mr = 41550 m= 2993 mr = 13316 m= 219 mr = 2173 m= 5 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 943 time to turn everything in is 0.7200000 number of dielectric boundary points 43291 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 14648 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) : 1.670551 object centre at (A) : 12.68850 21.21300 14.01650 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.3614243E-02 8.9893557E-02 midg,1,midg; midg,igrid,midg 1.1765487E-02 -8.4763885E-02 1,midg,midg; igrid,midg,midg -3.4635887E-02 -4.4022318E-02 gauss-seidel spectral radius is 0.9990888 estimated iterations to convergence 262 setup time was (sec) 0.9300000 now iterating at: 14:23:40 rms-change max change #iterations 6.948224 316.0225 at 10iterations 3.822781 105.9971 at 20iterations 2.078995 57.71773 at 30iterations 1.130146 28.48030 at 40iterations 0.6164693 17.68181 at 50iterations 0.3334112 9.391694 at 60iterations 0.1805104 4.507793 at 70iterations 9.7756036E-02 2.366590 at 80iterations 5.2972872E-02 1.296326 at 90iterations 2.8575651E-02 0.7146330 at 100iterations 1.5384238E-02 0.3932848 at 110iterations 8.3248019E-03 0.1951065 at 120iterations 4.4991532E-03 0.1140118 at 130iterations 2.4278401E-03 6.0240746E-02 at 140iterations 1.3118258E-03 3.3905029E-02 at 150iterations 7.0545543E-04 1.6346931E-02 at 160iterations 3.8115506E-04 9.0012550E-03 at 170iterations 2.0580692E-04 5.0468445E-03 at 180iterations finished qdiffx linear iterations at : 14:23:51 total time elapsed so far: 11.89000 # loops : 180 mean,max change (kT/e) : 2.0580692E-04 5.0468445E-03 energy calculations done at 11.89000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.03000 DelPhi exited at 14:23:51 12.040u 0.218s 0:12.54 97.6% 0+0k 0+45136io 0pf+0w