Sun Oct 9 09:12:03 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 09:12:03 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2658 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: 0.5836736 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): -78.59400 -31.47300 ymin,ymax (A): -34.00400 26.98900 zmin,zma (A): -50.02800 7.830000 x,y,z range (A): 47.12100 60.99300 57.85800 scale (grids/A): 0.5836736 object centre (A): -55.03350 -3.507499 -21.09900 number of atom coordinates read : 2658 total number of charged atoms : 2513 net assigned charge : -1.999981 assigned positive charge : 393.0337 centred at (gu) : 89.59339 89.42605 87.90060 assigned negative charge : -395.0345 centred at (gu) : 89.62051 89.60147 87.93277 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 6157 nv = 96 ne = 84 npr = 51841 no. pairs analyzed = 51841 no. exposed pairs = 3810 no. arc points = 27316 no. surface atoms = 1260 nbur = 1398 mkacc time = 9.0000004E-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 = 1.484000 m= 316 mr = 2992 m= 0 mr = 16 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1900000 number of dielectric boundary points 3465 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2652 ## 307 charges are in solution ## iepsmp to db, and charging done at 0.2500000 number of grid points assigned charge 7674 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.0216837E-10 -7.6807138E-10 midg,1,midg; midg,igrid,midg 3.7182941E-09 -3.9047530E-09 1,midg,midg; igrid,midg,midg 6.8519093E-11 -1.0299289E-09 gauss-seidel spectral radius is 0.9848348 estimated iterations to convergence 67 setup time was (sec) 0.3800000 now iterating at: 09:12:03 rms-change max change #iterations 9.5400855E-02 23.65403 at 10iterations 7.5261127E-03 1.340393 at 20iterations 5.9018965E-04 9.4811440E-02 at 30iterations 4.6698726E-05 7.8182220E-03 at 40iterations 3.7069306E-06 6.4086914E-04 at 50iterations finished qdiffx linear iterations at : 09:12:06 total time elapsed so far: 3.240000 # loops : 50 mean,max change (kT/e) : 3.7069306E-06 6.4086914E-04 energy calculations done at 3.240000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.370000 DelPhi exited at 09:12:07 3.375u 0.184s 0:03.86 91.9% 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 09:12:07 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2658 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: 1.751021 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): -78.59400 -31.47300 ymin,ymax (A): -34.00400 26.98900 zmin,zma (A): -50.02800 7.830000 x,y,z range (A): 47.12100 60.99300 57.85800 scale (grids/A): 1.751021 object centre (A): -55.03350 -3.507499 -21.09900 number of atom coordinates read : 2658 total number of charged atoms : 2513 net assigned charge : -1.999981 assigned positive charge : 393.0337 centred at (gu) : 88.77940 88.27751 83.70142 assigned negative charge : -395.0345 centred at (gu) : 88.86119 88.80399 83.79820 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 66900 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27316 grid for indexing accessible points = 1.400000 m= 22420 mr = 43302 m= 2906 mr = 15336 m= 131 mr = 1470 m= 0 mr = 23 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 32226 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 236 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 19560 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) : 0.5836736 object centre at (A) : -55.03350 -3.507499 -21.09900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -9.9467179E-03 -1.8267862E-04 midg,1,midg; midg,igrid,midg -6.7224614E-03 -2.2380883E-02 1,midg,midg; igrid,midg,midg 8.7206485E-03 4.4787014E-03 gauss-seidel spectral radius is 0.9984121 estimated iterations to convergence 199 setup time was (sec) 0.5400000 now iterating at: 09:12:08 rms-change max change #iterations 3.613278 162.2523 at 10iterations 1.583744 67.55235 at 20iterations 0.6926320 23.73679 at 30iterations 0.3058677 10.56442 at 40iterations 0.1346046 5.147814 at 50iterations 5.9080727E-02 2.188902 at 60iterations 2.6006879E-02 0.9024010 at 70iterations 1.1487647E-02 0.3758240 at 80iterations 5.0614001E-03 0.1766739 at 90iterations 2.2362191E-03 8.1927299E-02 at 100iterations 9.8368188E-04 4.2022705E-02 at 110iterations 4.3215539E-04 1.5020847E-02 at 120iterations finished qdiffx linear iterations at : 09:12:15 total time elapsed so far: 7.540000 # loops : 120 mean,max change (kT/e) : 4.3215539E-04 1.5020847E-02 energy calculations done at 7.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.680000 DelPhi exited at 09:12:15 7.678u 0.207s 0:08.19 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 09:12:15 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2658 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: 2.626531 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): -78.59400 -31.47300 ymin,ymax (A): -34.00400 26.98900 zmin,zma (A): -50.02800 7.830000 x,y,z range (A): 47.12100 60.99300 57.85800 scale (grids/A): 2.626531 object centre (A): -55.03350 -3.507499 -21.09900 number of atom coordinates read : 2658 total number of charged atoms : 2513 net assigned charge : -1.999981 assigned positive charge : 393.0337 centred at (gu) : 88.16891 87.41607 80.55196 assigned negative charge : -395.0345 centred at (gu) : 88.29175 88.20596 80.69722 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 154858 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27316 grid for indexing accessible points = 1.400000 m= 73370 mr = 106091 m= 24394 mr = 57371 m= 4869 mr = 18379 m= 470 mr = 3192 m= 10 mr = 239 m= 0 mr = 2 time to grow re-entrant surface = 0.4600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8200000 number of dielectric boundary points 72697 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 5 iepsmp to db, and charging done at 0.9100000 number of grid points assigned charge 20103 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) : 1.751021 object centre at (A) : -55.03350 -3.507499 -21.09900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1229843 -5.1823307E-02 midg,1,midg; midg,igrid,midg -0.1116711 1.4455488E-03 1,midg,midg; igrid,midg,midg 0.1308723 7.1280427E-02 gauss-seidel spectral radius is 0.9992078 estimated iterations to convergence 281 setup time was (sec) 1.060000 now iterating at: 09:12:16 rms-change max change #iterations 9.124497 324.8610 at 10iterations 5.291018 128.3321 at 20iterations 3.040957 70.90860 at 30iterations 1.739254 36.12007 at 40iterations 0.9885669 22.50429 at 50iterations 0.5612752 12.71542 at 60iterations 0.3178902 6.721258 at 70iterations 0.1801199 3.378315 at 80iterations 0.1016751 2.313245 at 90iterations 5.7397656E-02 1.233893 at 100iterations 3.2404501E-02 0.6631165 at 110iterations 1.8316122E-02 0.3632088 at 120iterations 1.0319769E-02 0.2083457 at 130iterations 5.7981312E-03 0.1197681 at 140iterations 3.2676826E-03 6.2540054E-02 at 150iterations 1.8436305E-03 3.4840584E-02 at 160iterations 1.0377089E-03 2.0446777E-02 at 170iterations 5.8590720E-04 1.2825727E-02 at 180iterations finished qdiffx linear iterations at : 09:12:28 total time elapsed so far: 12.29000 # loops : 180 mean,max change (kT/e) : 5.8590720E-04 1.2825727E-02 energy calculations done at 12.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.42000 DelPhi exited at 09:12:28 12.425u 0.217s 0:12.97 97.3% 0+0k 0+0io 0pf+0w