Tue Nov 22 14:12:35 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 Tue Nov 22 2011 at 14:12:40 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: 235 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1952 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: 0.5922475 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): -19.91700 40.19300 ymin,ymax (A): -17.71100 25.38200 zmin,zma (A): -18.14600 23.84500 x,y,z range (A): 60.11000 43.09300 41.99100 scale (grids/A): 0.5922475 object centre (A): 10.13800 3.835500 2.849500 number of atom coordinates read : 1952 total number of charged atoms : 1818 net assigned charge : -1.999997 assigned positive charge : 292.0978 centred at (gu) : 91.46766 89.20645 89.73560 assigned negative charge : -294.0981 centred at (gu) : 91.45274 89.19402 89.83591 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 4546 nv = 96 ne = 84 npr = 39670 no. pairs analyzed = 39670 no. exposed pairs = 2506 no. arc points = 17489 no. surface atoms = 854 nbur = 1098 mkacc time = 8.9999996E-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= 206 mr = 2407 m= 0 mr = 21 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 2 time to turn everything in is 0.2000000 number of dielectric boundary points 2324 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1767 ## 200 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 5621 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.5699807E-09 -2.6944298E-09 midg,1,midg; midg,igrid,midg -1.1241468E-09 -3.3874129E-10 1,midg,midg; igrid,midg,midg -7.1461248E-10 -4.7544269E-10 gauss-seidel spectral radius is 0.9851943 estimated iterations to convergence 67 setup time was (sec) 0.4100000 now iterating at: 14:12:45 rms-change max change #iterations 8.9641146E-02 15.80471 at 10iterations 7.4651516E-03 1.270893 at 20iterations 6.0318003E-04 9.8312855E-02 at 30iterations 4.8789407E-05 8.2206726E-03 at 40iterations 4.0750347E-06 7.7056885E-04 at 50iterations finished qdiffx linear iterations at : 14:12:53 total time elapsed so far: 2.900000 # loops : 50 mean,max change (kT/e) : 4.0750347E-06 7.7056885E-04 energy calculations done at 2.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.060000 DelPhi exited at 14:12:57 3.059u 0.186s 0:17.23 18.7% 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 Nov 22 2011 at 14:13:01 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: 235 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1952 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: 1.776743 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): -19.91700 40.19300 ymin,ymax (A): -17.71100 25.38200 zmin,zma (A): -18.14600 23.84500 x,y,z range (A): 60.11000 43.09300 41.99100 scale (grids/A): 1.776743 object centre (A): 10.13800 3.835500 2.849500 number of atom coordinates read : 1952 total number of charged atoms : 1818 net assigned charge : -1.999997 assigned positive charge : 292.0978 centred at (gu) : 94.40288 87.61938 89.20672 assigned negative charge : -294.0981 centred at (gu) : 94.35855 87.58205 89.50790 start vw surface at 0.1100000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 49389 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17489 grid for indexing accessible points = 1.400000 m= 16682 mr = 33357 m= 2219 mr = 12308 m= 92 mr = 1361 m= 0 mr = 20 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 552 time to turn everything in is 0.3500000 number of dielectric boundary points 21336 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 187 iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 14164 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) : 0.5922475 object centre at (A) : 10.13800 3.835500 2.849500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.1381756E-03 -5.8726156E-03 midg,1,midg; midg,igrid,midg -7.2674053E-03 -7.9162037E-03 1,midg,midg; igrid,midg,midg 1.2703588E-03 7.2617834E-03 gauss-seidel spectral radius is 0.9983534 estimated iterations to convergence 196 setup time was (sec) 0.6200000 now iterating at: 14:13:06 rms-change max change #iterations 3.154745 175.4106 at 10iterations 1.366769 60.34933 at 20iterations 0.5949750 23.82359 at 30iterations 0.2573956 11.19396 at 40iterations 0.1117455 4.516587 at 50iterations 4.8360273E-02 2.287788 at 60iterations 2.1069285E-02 0.8611374 at 70iterations 9.1914441E-03 0.3580017 at 80iterations 3.9884462E-03 0.1424760 at 90iterations 1.7326125E-03 6.5677643E-02 at 100iterations 7.5269461E-04 2.9678345E-02 at 110iterations 3.2523079E-04 1.2651205E-02 at 120iterations finished qdiffx linear iterations at : 14:13:25 total time elapsed so far: 6.600000 # loops : 120 mean,max change (kT/e) : 3.2523079E-04 1.2651205E-02 energy calculations done at 6.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.780000 DelPhi exited at 14:13:31 6.780u 0.150s 0:31.38 22.0% 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 Tue Nov 22 2011 at 14:13:36 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: 235 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1952 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: 2.665114 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): -19.91700 40.19300 ymin,ymax (A): -17.71100 25.38200 zmin,zma (A): -18.14600 23.84500 x,y,z range (A): 60.11000 43.09300 41.99100 scale (grids/A): 2.665114 object centre (A): 10.13800 3.835500 2.849500 number of atom coordinates read : 1952 total number of charged atoms : 1818 net assigned charge : -1.999997 assigned positive charge : 292.0978 centred at (gu) : 96.60425 86.42913 88.81010 assigned negative charge : -294.0981 centred at (gu) : 96.53777 86.37318 89.26192 start vw surface at 0.1100000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 114221 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17489 grid for indexing accessible points = 1.400000 m= 55119 mr = 81051 m= 18553 mr = 44862 m= 3795 mr = 15000 m= 412 mr = 2766 m= 18 mr = 296 m= 0 mr = 10 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 1671 time to turn everything in is 0.8400000 number of dielectric boundary points 48133 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 14543 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) : 1.776743 object centre at (A) : 10.13800 3.835500 2.849500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.8171794E-02 -7.6349489E-02 midg,1,midg; midg,igrid,midg -7.1061306E-02 -9.5054783E-02 1,midg,midg; igrid,midg,midg 4.0278565E-02 0.2750575 gauss-seidel spectral radius is 0.9991589 estimated iterations to convergence 272 setup time was (sec) 1.140000 now iterating at: 14:13:42 rms-change max change #iterations 7.700638 259.8480 at 10iterations 4.314936 117.1475 at 20iterations 2.392953 57.47075 at 30iterations 1.323321 31.73254 at 40iterations 0.7327229 16.47572 at 50iterations 0.4050591 9.139009 at 60iterations 0.2243207 5.126163 at 70iterations 0.1238688 2.714767 at 80iterations 6.8626054E-02 1.668110 at 90iterations 3.7815727E-02 0.8738296 at 100iterations 2.0914122E-02 0.4600258 at 110iterations 1.1566238E-02 0.2509823 at 120iterations 6.3703358E-03 0.1339626 at 130iterations 3.5137376E-03 8.6665154E-02 at 140iterations 1.9452408E-03 4.2649984E-02 at 150iterations 1.0754584E-03 2.5842190E-02 at 160iterations 5.9390790E-04 1.3141632E-02 at 170iterations 3.2840332E-04 7.5359344E-03 at 180iterations finished qdiffx linear iterations at : 14:14:05 total time elapsed so far: 11.24000 # loops : 180 mean,max change (kT/e) : 3.2840332E-04 7.5359344E-03 energy calculations done at 11.24000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.40000 DelPhi exited at 14:14:11 11.404u 0.197s 0:35.40 32.7% 0+0k 0+0io 0pf+0w