Tue Oct 11 06:16:45 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 Tue Oct 11 2011 at 06:16:45 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2014 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: 0.7299869 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): -19.89400 24.18300 ymin,ymax (A): -11.11400 28.62200 zmin,zma (A): -2.690000 46.07800 x,y,z range (A): 44.07700 39.73600 48.76800 scale (grids/A): 0.7299869 object centre (A): 2.144501 8.754000 21.69400 number of atom coordinates read : 2014 total number of charged atoms : 1890 net assigned charge : 6.500007 assigned positive charge : 307.8402 centred at (gu) : 89.97951 89.42683 90.97339 assigned negative charge : -301.3401 centred at (gu) : 89.81896 89.46783 91.06566 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 7419 nv = 96 ne = 84 npr = 40306 no. pairs analyzed = 40306 no. exposed pairs = 2424 no. arc points = 16754 no. surface atoms = 834 nbur = 1180 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 557 mr = 4330 m= 10 mr = 131 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3525 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1548 ## 158 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 7970 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.3651592E-07 2.3269985E-08 midg,1,midg; midg,igrid,midg 1.3837339E-07 5.4854052E-08 1,midg,midg; igrid,midg,midg -3.4201999E-08 2.1460819E-07 gauss-seidel spectral radius is 0.9902074 estimated iterations to convergence 82 setup time was (sec) 0.6900000 now iterating at: 06:16:46 rms-change max change #iterations 0.2314778 30.55037 at 10iterations 3.0501852E-02 3.784340 at 20iterations 4.1228463E-03 0.6208649 at 30iterations 6.2937231E-04 8.2124710E-02 at 40iterations 1.3009904E-04 1.7465591E-02 at 50iterations finished qdiffx linear iterations at : 06:16:50 total time elapsed so far: 4.520000 # loops : 50 mean,max change (kT/e) : 1.3009904E-04 1.7465591E-02 energy calculations done at 4.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.750000 DelPhi exited at 06:16:51 4.751u 0.423s 0:05.71 90.5% 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 06:16:51 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2014 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: 2.189961 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): -19.89400 24.18300 ymin,ymax (A): -11.11400 28.62200 zmin,zma (A): -2.690000 46.07800 x,y,z range (A): 44.07700 39.73600 48.76800 scale (grids/A): 2.189961 object centre (A): 2.144501 8.754000 21.69400 number of atom coordinates read : 2014 total number of charged atoms : 1890 net assigned charge : 6.500007 assigned positive charge : 307.8402 centred at (gu) : 89.93878 88.28070 92.92022 assigned negative charge : -301.3401 centred at (gu) : 89.45688 88.40339 93.19705 start vw surface at 0.1300000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 77610 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16754 grid for indexing accessible points = 1.400000 m= 33434 mr = 55358 m= 7634 mr = 26010 m= 853 mr = 5416 m= 32 mr = 508 m= 1 mr = 8 m= 0 mr = 0 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8300000 number of dielectric boundary points 32264 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 65 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 15026 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) : 0.7299869 object centre at (A) : 2.144501 8.754000 21.69400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.0242720E-02 1.1185676E-02 midg,1,midg; midg,igrid,midg 4.2568035E-02 6.9919270E-03 1,midg,midg; igrid,midg,midg 2.2859193E-02 5.5957001E-02 gauss-seidel spectral radius is 0.9988859 estimated iterations to convergence 237 setup time was (sec) 1.180000 now iterating at: 06:16:53 rms-change max change #iterations 4.835843 192.4299 at 10iterations 2.429568 74.22398 at 20iterations 1.230743 35.63272 at 30iterations 0.6215354 18.45509 at 40iterations 0.3137535 9.881932 at 50iterations 0.1590654 4.611983 at 60iterations 8.0216236E-02 2.378281 at 70iterations 4.0644106E-02 1.183852 at 80iterations 2.0509452E-02 0.5980988 at 90iterations 1.0433537E-02 0.3166542 at 100iterations 5.2999775E-03 0.1580992 at 110iterations 2.7236254E-03 9.3963623E-02 at 120iterations finished qdiffx linear iterations at : 06:17:03 total time elapsed so far: 11.20000 # loops : 120 mean,max change (kT/e) : 2.7236254E-03 9.3963623E-02 energy calculations done at 11.20000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.43000 DelPhi exited at 06:17:03 11.431u 0.477s 0:12.23 97.3% 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 06:17:03 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: 287 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2014 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: 3.284941 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): -19.89400 24.18300 ymin,ymax (A): -11.11400 28.62200 zmin,zma (A): -2.690000 46.07800 x,y,z range (A): 44.07700 39.73600 48.76800 scale (grids/A): 3.284941 object centre (A): 2.144501 8.754000 21.69400 number of atom coordinates read : 2014 total number of charged atoms : 1890 net assigned charge : 6.500007 assigned positive charge : 307.8402 centred at (gu) : 89.90807 87.42097 94.38029 assigned negative charge : -301.3401 centred at (gu) : 89.18548 87.60519 94.79552 start vw surface at 0.1300000 fill in re-entrant regions at 1.020000 boundary points on vw surface= 178543 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16754 grid for indexing accessible points = 1.400000 m= 101232 mr = 132855 m= 45162 mr = 85348 m= 14940 mr = 37976 m= 3433 mr = 12026 m= 493 mr = 2622 m= 22 mr = 329 m= 2 mr = 6 m= 0 mr = 0 time to grow re-entrant surface = 1.440000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 2.610000 number of dielectric boundary points 72665 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.790000 number of grid points assigned charge 15118 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) : 2.189961 object centre at (A) : 2.144501 8.754000 21.69400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2588257 2.8182726E-02 midg,1,midg; midg,igrid,midg 0.3420714 2.8462928E-02 1,midg,midg; igrid,midg,midg 0.3417724 0.4479837 gauss-seidel spectral radius is 0.9993073 estimated iterations to convergence 300 setup time was (sec) 3.010000 now iterating at: 06:17:07 rms-change max change #iterations 10.60450 416.2740 at 10iterations 6.318912 137.6441 at 20iterations 3.760793 76.45365 at 30iterations 2.229622 42.95390 at 40iterations 1.323279 22.44138 at 50iterations 0.7798439 14.51320 at 60iterations 0.4601648 7.845322 at 70iterations 0.2718746 4.583323 at 80iterations 0.1604068 2.693131 at 90iterations 9.4597027E-02 1.738972 at 100iterations 5.5660155E-02 0.9528122 at 110iterations 3.2896668E-02 0.6555762 at 120iterations 1.9540684E-02 0.3420944 at 130iterations 1.1651266E-02 0.2080536 at 140iterations 7.1118968E-03 0.1265838 at 150iterations 4.4560130E-03 8.7737560E-02 at 160iterations 2.9145833E-03 5.3985596E-02 at 170iterations 2.0305680E-03 3.6085129E-02 at 180iterations finished qdiffx linear iterations at : 06:17:24 total time elapsed so far: 19.97000 # loops : 180 mean,max change (kT/e) : 2.0305680E-03 3.6085129E-02 energy calculations done at 19.97000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 20.20000 DelPhi exited at 06:17:24 20.203u 0.499s 0:21.08 98.1% 0+0k 0+0io 0pf+0w