Tue Oct 11 01:35:50 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 Tue Oct 11 2011 at 01:35:50 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 = 3948 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: 0.5163237 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): 1.407000 65.83600 ymin,ymax (A): 8.169001 75.91300 zmin,zma (A): 17.55500 86.50400 x,y,z range (A): 64.42900 67.74400 68.94900 scale (grids/A): 0.5163237 object centre (A): 33.62150 42.04100 52.02950 number of atom coordinates read : 3948 total number of charged atoms : 3795 net assigned charge : 5.000027 assigned positive charge : 603.7202 centred at (gu) : 89.51218 91.08576 87.69470 assigned negative charge : -598.7225 centred at (gu) : 89.40286 91.14825 87.79670 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6564 nv = 96 ne = 84 npr = 78569 no. pairs analyzed = 78569 no. exposed pairs = 5062 no. arc points = 35934 no. surface atoms = 1697 nbur = 2251 mkacc time = 0.2100000 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 = 1.652000 m= 226 mr = 3225 m= 1 mr = 12 m= 0 mr = 0 time to grow re-entrant surface = 0.2500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4300000 number of dielectric boundary points 3554 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3504 ## 535 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 8889 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 6.7116673E-10 -1.0623803E-10 midg,1,midg; midg,igrid,midg 1.9449538E-10 -1.1598353E-10 1,midg,midg; igrid,midg,midg -2.4791827E-10 3.3751196E-10 gauss-seidel spectral radius is 0.9807564 estimated iterations to convergence 60 setup time was (sec) 0.7100000 now iterating at: 01:35:51 rms-change max change #iterations 6.4716995E-02 10.82930 at 10iterations 4.7427495E-03 0.9376564 at 20iterations 6.4001197E-04 0.1721039 at 30iterations 1.2423319E-04 3.3908844E-02 at 40iterations 2.4989449E-05 6.8130493E-03 at 50iterations finished qdiffx linear iterations at : 01:35:55 total time elapsed so far: 4.480000 # loops : 50 mean,max change (kT/e) : 2.4989449E-05 6.8130493E-03 energy calculations done at 4.480000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.670000 DelPhi exited at 01:35:56 4.676u 0.374s 0:05.74 87.8% 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 01:35:56 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 = 3948 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: 1.548971 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): 1.407000 65.83600 ymin,ymax (A): 8.169001 75.91300 zmin,zma (A): 17.55500 86.50400 x,y,z range (A): 64.42900 67.74400 68.94900 scale (grids/A): 1.548971 object centre (A): 33.62150 42.04100 52.02950 number of atom coordinates read : 3948 total number of charged atoms : 3795 net assigned charge : 5.000027 assigned positive charge : 603.7202 centred at (gu) : 88.53568 93.25645 83.08327 assigned negative charge : -598.7225 centred at (gu) : 88.20827 93.44437 83.38968 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 73842 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35934 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 19978 mr = 48768 m= 1679 mr = 13098 m= 23 mr = 684 m= 0 mr = 5 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 1909 time to turn everything in is 0.6200000 number of dielectric boundary points 32967 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 455 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7500000 number of grid points assigned charge 28576 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) : 0.5163237 object centre at (A) : 33.62150 42.04100 52.02950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1691077E-02 -2.9349776E-02 midg,1,midg; midg,igrid,midg 1.5842956E-02 1.1896335E-02 1,midg,midg; igrid,midg,midg -9.5333189E-06 4.2884052E-03 gauss-seidel spectral radius is 0.9980565 estimated iterations to convergence 180 setup time was (sec) 0.9400000 now iterating at: 01:35:57 rms-change max change #iterations 3.488050 201.5237 at 10iterations 1.404309 54.57382 at 20iterations 0.5655103 18.85516 at 30iterations 0.2287026 7.589703 at 40iterations 9.2834428E-02 3.176610 at 50iterations 3.7574325E-02 1.526054 at 60iterations 1.5348686E-02 0.5466232 at 70iterations 6.3254195E-03 0.2794342 at 80iterations 2.6325141E-03 9.7461700E-02 at 90iterations 1.1440171E-03 5.4378510E-02 at 100iterations 5.1387498E-04 2.3246765E-02 at 110iterations 2.4569916E-04 1.3549805E-02 at 120iterations finished qdiffx linear iterations at : 01:36:06 total time elapsed so far: 10.40000 # loops : 120 mean,max change (kT/e) : 2.4569916E-04 1.3549805E-02 energy calculations done at 10.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.57000 DelPhi exited at 01:36:07 10.575u 0.472s 0:11.77 93.7% 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 Oct 11 2011 at 01:36:07 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3948 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: 2.323457 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): 1.407000 65.83600 ymin,ymax (A): 8.169001 75.91300 zmin,zma (A): 17.55500 86.50400 x,y,z range (A): 64.42900 67.74400 68.94900 scale (grids/A): 2.323457 object centre (A): 33.62150 42.04100 52.02950 number of atom coordinates read : 3948 total number of charged atoms : 3795 net assigned charge : 5.000027 assigned positive charge : 603.7202 centred at (gu) : 87.80304 94.88443 79.62469 assigned negative charge : -598.7225 centred at (gu) : 87.31263 95.16628 80.08445 start vw surface at 0.1400000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 172427 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35934 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 72165 mr = 120629 m= 17927 mr = 55434 m= 2337 mr = 12945 m= 102 mr = 1414 m= 0 mr = 49 time to grow re-entrant surface = 0.8800001 no. cavity mid-points inaccessible to solvent = 6707 time to turn everything in is 1.510000 number of dielectric boundary points 74487 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 50 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 30276 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) : 1.548971 object centre at (A) : 33.62150 42.04100 52.02950 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1391565 -0.4256983 midg,1,midg; midg,igrid,midg 0.3080004 0.1589587 1,midg,midg; igrid,midg,midg 0.1488177 0.1242743 gauss-seidel spectral radius is 0.9991143 estimated iterations to convergence 265 setup time was (sec) 1.860000 now iterating at: 01:36:10 rms-change max change #iterations 9.385001 274.4032 at 10iterations 5.236418 164.8932 at 20iterations 2.910109 74.92783 at 30iterations 1.604528 40.35650 at 40iterations 0.8835027 18.39688 at 50iterations 0.4858221 11.13319 at 60iterations 0.2663425 5.255173 at 70iterations 0.1458803 2.901310 at 80iterations 7.9711318E-02 1.836794 at 90iterations 4.3688051E-02 0.8485322 at 100iterations 2.3918049E-02 0.4774971 at 110iterations 1.3084075E-02 0.2485714 at 120iterations 7.1712243E-03 0.1627083 at 130iterations 3.9442056E-03 8.6502075E-02 at 140iterations 2.1851601E-03 4.9674988E-02 at 150iterations 1.2183913E-03 2.6657104E-02 at 160iterations 6.9084828E-04 1.8463135E-02 at 170iterations 3.9814363E-04 1.0490417E-02 at 180iterations finished qdiffx linear iterations at : 01:36:29 total time elapsed so far: 20.65000 # loops : 180 mean,max change (kT/e) : 3.9814363E-04 1.0490417E-02 energy calculations done at 20.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.81000 DelPhi exited at 01:36:30 20.819u 0.587s 0:22.75 94.0% 0+0k 0+0io 0pf+0w