Mon Oct 10 17:03:19 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 Mon Oct 10 2011 at 17:03:19 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2815 !!! WARNING: HIT 107 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6199822 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): -8.526000 48.89500 ymin,ymax (A): -8.139000 39.32800 zmin,zma (A): -0.2900000 54.94200 x,y,z range (A): 57.42100 47.46700 55.23200 scale (grids/A): 0.6199822 object centre (A): 20.18450 15.59450 27.32600 number of atom coordinates read : 2815 total number of charged atoms : 2674 net assigned charge : -2.985975 assigned positive charge : 425.5041 centred at (gu) : 89.00183 89.46638 89.15425 assigned negative charge : -428.4912 centred at (gu) : 88.89651 89.36118 89.11855 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7357 nv = 96 ne = 84 npr = 55359 no. pairs analyzed = 55359 no. exposed pairs = 3782 no. arc points = 26692 no. surface atoms = 1270 nbur = 1545 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 352 mr = 3868 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 40 time to turn everything in is 0.3000000 number of dielectric boundary points 3823 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2597 ## 254 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8948 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.8485696E-09 2.8723354E-10 midg,1,midg; midg,igrid,midg -1.1287933E-08 4.7591500E-09 1,midg,midg; igrid,midg,midg -1.2537496E-08 4.2887907E-09 gauss-seidel spectral radius is 0.9865553 estimated iterations to convergence 71 setup time was (sec) 0.5700000 now iterating at: 17:03:19 rms-change max change #iterations 0.1306915 19.24132 at 10iterations 1.1932397E-02 1.832783 at 20iterations 1.0952186E-03 0.1779385 at 30iterations 1.0107464E-04 1.4926910E-02 at 40iterations 9.2963865E-06 1.3771057E-03 at 50iterations finished qdiffx linear iterations at : 17:03:23 total time elapsed so far: 3.980000 # loops : 50 mean,max change (kT/e) : 9.2963865E-06 1.3771057E-03 energy calculations done at 3.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.160000 DelPhi exited at 17:03:24 4.168u 0.232s 0:05.03 87.2% 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 Mon Oct 10 2011 at 17:03:24 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2815 !!! WARNING: HIT 107 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.859947 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): -8.526000 48.89500 ymin,ymax (A): -8.139000 39.32800 zmin,zma (A): -0.2900000 54.94200 x,y,z range (A): 57.42100 47.46700 55.23200 scale (grids/A): 1.859947 object centre (A): 20.18450 15.59450 27.32600 number of atom coordinates read : 2815 total number of charged atoms : 2674 net assigned charge : -2.985975 assigned positive charge : 425.5041 centred at (gu) : 87.00488 88.39823 87.46163 assigned negative charge : -428.4912 centred at (gu) : 86.68909 88.08325 87.35535 start vw surface at 0.1400000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 79850 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26692 grid for indexing accessible points = 1.400000 m= 26809 mr = 53919 m= 3677 mr = 19009 m= 164 mr = 2052 m= 2 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 1417 time to turn everything in is 0.5800000 number of dielectric boundary points 35480 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 193 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 20951 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) : 0.6199822 object centre at (A) : 20.18450 15.59450 27.32600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.5734253E-03 -7.4707251E-04 midg,1,midg; midg,igrid,midg -2.2060115E-02 5.3080975E-04 1,midg,midg; igrid,midg,midg -5.4460380E-02 2.9383389E-02 gauss-seidel spectral radius is 0.9986025 estimated iterations to convergence 212 setup time was (sec) 0.9000000 now iterating at: 17:03:25 rms-change max change #iterations 4.300390 159.6577 at 10iterations 1.994172 67.96602 at 20iterations 0.9218826 34.10518 at 30iterations 0.4261543 15.42953 at 40iterations 0.1977760 6.101109 at 50iterations 9.1421098E-02 2.622386 at 60iterations 4.2404283E-02 1.352409 at 70iterations 1.9647647E-02 0.7312380 at 80iterations 9.1033773E-03 0.2948503 at 90iterations 4.2222952E-03 0.1358814 at 100iterations 1.9579979E-03 6.2282562E-02 at 110iterations 9.1004011E-04 3.1416893E-02 at 120iterations finished qdiffx linear iterations at : 17:03:33 total time elapsed so far: 9.420000 # loops : 120 mean,max change (kT/e) : 9.1004011E-04 3.1416893E-02 energy calculations done at 9.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.590000 DelPhi exited at 17:03:34 9.596u 0.274s 0:10.57 93.2% 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 Mon Oct 10 2011 at 17:03:34 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2815 !!! WARNING: HIT 107 has a net charge of 0.5140 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.789920 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): -8.526000 48.89500 ymin,ymax (A): -8.139000 39.32800 zmin,zma (A): -0.2900000 54.94200 x,y,z range (A): 57.42100 47.46700 55.23200 scale (grids/A): 2.789920 object centre (A): 20.18450 15.59450 27.32600 number of atom coordinates read : 2815 total number of charged atoms : 2674 net assigned charge : -2.985975 assigned positive charge : 425.5041 centred at (gu) : 85.50708 87.59732 86.19227 assigned negative charge : -428.4912 centred at (gu) : 85.03355 87.12478 86.03288 start vw surface at 0.1500000 fill in re-entrant regions at 0.4900000 boundary points on vw surface= 184905 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26692 grid for indexing accessible points = 1.400000 m= 88365 mr = 131366 m= 29344 mr = 70602 m= 6288 mr = 22922 m= 704 mr = 4409 m= 23 mr = 392 m= 0 mr = 6 time to grow re-entrant surface = 0.8900000 no. cavity mid-points inaccessible to solvent = 4533 time to turn everything in is 1.500000 number of dielectric boundary points 79932 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.660000 number of grid points assigned charge 21389 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) : 1.859947 object centre at (A) : 20.18450 15.59450 27.32600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1328268 -0.2359328 midg,1,midg; midg,igrid,midg -0.2138555 -3.5983238E-02 1,midg,midg; igrid,midg,midg -0.6226324 0.3780543 gauss-seidel spectral radius is 0.9992682 estimated iterations to convergence 292 setup time was (sec) 1.860000 now iterating at: 17:03:36 rms-change max change #iterations 10.36161 367.7419 at 10iterations 6.151257 161.6985 at 20iterations 3.613000 96.29724 at 30iterations 2.116044 49.35930 at 40iterations 1.232337 28.43204 at 50iterations 0.7164851 16.11900 at 60iterations 0.4152054 8.219740 at 70iterations 0.2407464 4.761635 at 80iterations 0.1392501 2.683877 at 90iterations 8.0350362E-02 1.545419 at 100iterations 4.6420109E-02 0.8685799 at 110iterations 2.6780495E-02 0.4635239 at 120iterations 1.5456277E-02 0.2746506 at 130iterations 8.9322757E-03 0.1719170 at 140iterations 5.1429928E-03 9.7356796E-02 at 150iterations 2.9697591E-03 5.5081129E-02 at 160iterations 1.7104775E-03 3.3635557E-02 at 170iterations 9.8598376E-04 1.6739845E-02 at 180iterations finished qdiffx linear iterations at : 17:03:50 total time elapsed so far: 15.50000 # loops : 180 mean,max change (kT/e) : 9.8598376E-04 1.6739845E-02 energy calculations done at 15.50000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.68000 DelPhi exited at 17:03:52 15.685u 0.260s 0:17.25 92.4% 0+0k 0+0io 0pf+0w