Sun Oct 9 09:05:36 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+sph.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 = amb.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 09:05:36 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2559 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.5231217 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): -14.04400 54.00900 ymin,ymax (A): -27.49900 34.97300 zmin,zma (A): 31.34100 81.40300 x,y,z range (A): 68.05300 62.47200 50.06200 scale (grids/A): 0.5231217 object centre (A): 19.98250 3.737001 56.37200 number of atom coordinates read : 2559 total number of charged atoms : 2415 net assigned charge : 7.500015 assigned positive charge : 376.8390 centred at (gu) : 93.63156 91.59539 90.74191 assigned negative charge : -369.3396 centred at (gu) : 93.58971 91.63564 90.73555 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 4687 nv = 96 ne = 84 npr = 49346 no. pairs analyzed = 49346 no. exposed pairs = 3649 no. arc points = 26367 no. surface atoms = 1202 nbur = 1357 mkacc time = 0.1100000 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 = 1.624000 m= 168 mr = 2139 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 2716 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2557 ## 387 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 6087 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3593768E-10 2.3082383E-10 midg,1,midg; midg,igrid,midg 1.7814793E-10 1.2887415E-10 1,midg,midg; igrid,midg,midg 3.6255811E-11 6.9166778E-10 gauss-seidel spectral radius is 0.9811583 estimated iterations to convergence 60 setup time was (sec) 0.5200000 now iterating at: 09:05:37 rms-change max change #iterations 5.3449918E-02 11.41998 at 10iterations 3.0818575E-03 0.6244202 at 20iterations 2.3575875E-04 5.4262161E-02 at 30iterations 4.6779369E-05 1.4594078E-02 at 40iterations 1.3487567E-05 4.2629242E-03 at 50iterations finished qdiffx linear iterations at : 09:05:39 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 1.3487567E-05 4.2629242E-03 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.090000 DelPhi exited at 09:05:40 3.090u 0.125s 0:03.52 91.1% 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 09:05:40 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2559 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: 1.569365 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): -14.04400 54.00900 ymin,ymax (A): -27.49900 34.97300 zmin,zma (A): 31.34100 81.40300 x,y,z range (A): 68.05300 62.47200 50.06200 scale (grids/A): 1.569365 object centre (A): 19.98250 3.737001 56.37200 number of atom coordinates read : 2559 total number of charged atoms : 2415 net assigned charge : 7.500015 assigned positive charge : 376.8390 centred at (gu) : 100.8939 94.78570 92.22514 assigned negative charge : -369.3396 centred at (gu) : 100.7690 94.90662 92.20663 start vw surface at 0.1600000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 51521 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26367 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 14965 mr = 32435 m= 1414 mr = 9658 m= 35 mr = 523 m= 0 mr = 2 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4100000 number of dielectric boundary points 25317 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 355 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 18271 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) : 0.5231217 object centre at (A) : 19.98250 3.737001 56.37200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.5384496E-03 6.9695823E-03 midg,1,midg; midg,igrid,midg 8.7806424E-03 2.6995619E-03 1,midg,midg; igrid,midg,midg -8.2288273E-03 -2.6233764E-03 gauss-seidel spectral radius is 0.9979818 estimated iterations to convergence 177 setup time was (sec) 0.6900000 now iterating at: 09:05:41 rms-change max change #iterations 2.705515 136.2846 at 10iterations 1.066238 50.42530 at 20iterations 0.4214251 17.27553 at 30iterations 0.1666886 8.426155 at 40iterations 6.6286646E-02 2.660816 at 50iterations 2.6268590E-02 1.094290 at 60iterations 1.0447661E-02 0.4164457 at 70iterations 4.1690767E-03 0.1786385 at 80iterations 1.6690640E-03 7.1165085E-02 at 90iterations 6.8762520E-04 3.2161713E-02 at 100iterations 2.9518607E-04 1.5262604E-02 at 110iterations 1.3801019E-04 8.1396103E-03 at 120iterations finished qdiffx linear iterations at : 09:05:47 total time elapsed so far: 6.640000 # loops : 120 mean,max change (kT/e) : 1.3801019E-04 8.1396103E-03 energy calculations done at 6.640000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.810000 DelPhi exited at 09:05:47 6.814u 0.175s 0:07.30 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 Sun Oct 9 2011 at 09:05:47 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2559 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: 2.354048 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): -14.04400 54.00900 ymin,ymax (A): -27.49900 34.97300 zmin,zma (A): 31.34100 81.40300 x,y,z range (A): 68.05300 62.47200 50.06200 scale (grids/A): 2.354048 object centre (A): 19.98250 3.737001 56.37200 number of atom coordinates read : 2559 total number of charged atoms : 2415 net assigned charge : 7.500015 assigned positive charge : 376.8390 centred at (gu) : 106.3409 97.17836 93.33768 assigned negative charge : -369.3396 centred at (gu) : 106.1534 97.35989 93.30974 start vw surface at 0.1500000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 119645 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26367 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 52166 mr = 80347 m= 13998 mr = 39405 m= 1870 mr = 9895 m= 104 mr = 1027 m= 0 mr = 34 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8800000 number of dielectric boundary points 57075 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 19281 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) : 1.569365 object centre at (A) : 19.98250 3.737001 56.37200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2832997E-02 0.1148552 midg,1,midg; midg,igrid,midg 0.2844104 3.1809248E-02 1,midg,midg; igrid,midg,midg -0.1845815 -7.8554593E-02 gauss-seidel spectral radius is 0.9990520 estimated iterations to convergence 257 setup time was (sec) 1.150000 now iterating at: 09:05:49 rms-change max change #iterations 7.289807 363.4344 at 10iterations 4.001375 115.4788 at 20iterations 2.175212 63.16631 at 30iterations 1.174062 32.16311 at 40iterations 0.6330476 18.95259 at 50iterations 0.3395754 8.166638 at 60iterations 0.1820335 4.555552 at 70iterations 9.7302906E-02 2.379233 at 80iterations 5.2207988E-02 1.403534 at 90iterations 2.7813423E-02 0.6559019 at 100iterations 1.4888483E-02 0.3473663 at 110iterations 7.9529993E-03 0.1838703 at 120iterations 4.2494261E-03 9.8597527E-02 at 130iterations 2.2647418E-03 5.4442406E-02 at 140iterations 1.2120166E-03 2.9003143E-02 at 150iterations 6.4791093E-04 1.4824867E-02 at 160iterations 3.4890955E-04 9.1419220E-03 at 170iterations 1.8977244E-04 4.4517517E-03 at 180iterations finished qdiffx linear iterations at : 09:05:58 total time elapsed so far: 10.65000 # loops : 180 mean,max change (kT/e) : 1.8977244E-04 4.4517517E-03 energy calculations done at 10.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.82000 DelPhi exited at 09:05:59 10.825u 0.236s 0:11.33 97.5% 0+0k 0+0io 0pf+0w