Wed Feb 15 08:55:39 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:55:40 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 = 2417 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: 0.7001395 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): -14.58300 31.95400 ymin,ymax (A): -6.962000 40.17600 zmin,zma (A): 34.89500 85.74200 x,y,z range (A): 46.53700 47.13800 50.84701 scale (grids/A): 0.7001395 object centre (A): 8.685501 16.60700 60.31850 number of atom coordinates read : 2417 total number of charged atoms : 2280 net assigned charge : 1.000006 assigned positive charge : 359.9708 centred at (gu) : 89.28369 91.67886 88.95161 assigned negative charge : -358.9715 centred at (gu) : 89.42882 91.68008 88.91543 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8238 nv = 96 ne = 84 npr = 49725 no. pairs analyzed = 49725 no. exposed pairs = 3137 no. arc points = 21614 no. surface atoms = 1058 nbur = 1359 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 603 mr = 4607 m= 6 mr = 106 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.3100000 number of dielectric boundary points 4134 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1973 ## 158 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 9089 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.3328417E-08 1.9600350E-08 midg,1,midg; midg,igrid,midg 5.3626086E-09 8.4936769E-09 1,midg,midg; igrid,midg,midg 8.7197414E-08 -5.5372425E-08 gauss-seidel spectral radius is 0.9894100 estimated iterations to convergence 79 setup time was (sec) 0.5500000 now iterating at: 08:55:40 rms-change max change #iterations 0.2014212 24.97004 at 10iterations 2.4186555E-02 2.970085 at 20iterations 3.0418134E-03 0.3762360 at 30iterations 4.4851832E-04 6.3123703E-02 at 40iterations 1.0451522E-04 1.5591621E-02 at 50iterations finished qdiffx linear iterations at : 08:55:43 total time elapsed so far: 3.270000 # loops : 50 mean,max change (kT/e) : 1.0451522E-04 1.5591621E-02 energy calculations done at 3.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.470000 DelPhi exited at 08:55:44 3.475u 0.178s 0:04.51 80.7% 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 Wed Feb 15 2012 at 08:55:44 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 = 2417 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: 2.100419 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): -14.58300 31.95400 ymin,ymax (A): -6.962000 40.17600 zmin,zma (A): 34.89500 85.74200 x,y,z range (A): 46.53700 47.13800 50.84701 scale (grids/A): 2.100419 object centre (A): 8.685501 16.60700 60.31850 number of atom coordinates read : 2417 total number of charged atoms : 2280 net assigned charge : 1.000006 assigned positive charge : 359.9708 centred at (gu) : 87.85020 95.03576 86.85397 assigned negative charge : -358.9715 centred at (gu) : 88.28634 95.04004 86.74578 start vw surface at 0.1700000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 87149 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21614 grid for indexing accessible points = 1.400000 m= 35387 mr = 60665 m= 7242 mr = 26603 m= 680 mr = 4827 m= 17 mr = 321 m= 0 mr = 0 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 396 time to turn everything in is 0.7200000 number of dielectric boundary points 38059 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 85 iepsmp to db, and charging done at 0.8600000 number of grid points assigned charge 18090 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) : 0.7001395 object centre at (A) : 8.685501 16.60700 60.31850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4922202E-03 2.8073525E-02 midg,1,midg; midg,igrid,midg -1.1471549E-04 -1.1114360E-02 1,midg,midg; igrid,midg,midg 3.0146027E-02 -1.8351257E-02 gauss-seidel spectral radius is 0.9988512 estimated iterations to convergence 234 setup time was (sec) 1.050000 now iterating at: 08:55:45 rms-change max change #iterations 4.918787 212.7650 at 10iterations 2.442748 70.02400 at 20iterations 1.223751 34.87811 at 30iterations 0.6103426 17.86041 at 40iterations 0.3048510 8.926500 at 50iterations 0.1524259 4.453613 at 60iterations 7.6264523E-02 2.194458 at 70iterations 3.7950791E-02 1.068815 at 80iterations 1.8970180E-02 0.5419712 at 90iterations 9.5397532E-03 0.3092203 at 100iterations 4.8095104E-03 0.1408749 at 110iterations 2.4383585E-03 7.3747635E-02 at 120iterations finished qdiffx linear iterations at : 08:55:53 total time elapsed so far: 8.390000 # loops : 120 mean,max change (kT/e) : 2.4383585E-03 7.3747635E-02 energy calculations done at 8.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.600000 DelPhi exited at 08:55:54 8.598u 0.235s 0:09.68 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 Wed Feb 15 2012 at 08:55:54 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 = 2417 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 3.150628 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): -14.58300 31.95400 ymin,ymax (A): -6.962000 40.17600 zmin,zma (A): 34.89500 85.74200 x,y,z range (A): 46.53700 47.13800 50.84701 scale (grids/A): 3.150628 object centre (A): 8.685501 16.60700 60.31850 number of atom coordinates read : 2417 total number of charged atoms : 2280 net assigned charge : 1.000006 assigned positive charge : 359.9708 centred at (gu) : 86.77504 97.55355 85.28074 assigned negative charge : -358.9715 centred at (gu) : 87.42936 97.55994 85.11856 start vw surface at 0.2000000 fill in re-entrant regions at 0.9900000 boundary points on vw surface= 200909 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21614 grid for indexing accessible points = 1.400000 m= 108786 mr = 146272 m= 45931 mr = 90046 m= 13674 mr = 37501 m= 2790 mr = 10584 m= 282 mr = 1981 m= 3 mr = 165 m= 0 mr = 0 time to grow re-entrant surface = 1.150000 no. cavity mid-points inaccessible to solvent = 1359 time to turn everything in is 2.310000 number of dielectric boundary points 85826 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 2.470000 number of grid points assigned charge 18236 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) : 2.100419 object centre at (A) : 8.685501 16.60700 60.31850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1932908 0.6378857 midg,1,midg; midg,igrid,midg -0.1168057 -8.7976627E-02 1,midg,midg; igrid,midg,midg 0.2272363 -0.1774438 gauss-seidel spectral radius is 0.9993174 estimated iterations to convergence 302 setup time was (sec) 2.650000 now iterating at: 08:55:57 rms-change max change #iterations 11.18275 357.4406 at 10iterations 6.711786 167.3207 at 20iterations 4.017346 85.34517 at 30iterations 2.394525 43.67830 at 40iterations 1.424340 26.50934 at 50iterations 0.8452858 15.14223 at 60iterations 0.5004118 8.398596 at 70iterations 0.2960300 5.854169 at 80iterations 0.1746034 3.637442 at 90iterations 0.1030433 1.740362 at 100iterations 6.0600586E-02 1.116285 at 110iterations 3.5735302E-02 0.5845499 at 120iterations 2.1024525E-02 0.3266907 at 130iterations 1.2389252E-02 0.2040405 at 140iterations 7.2769090E-03 0.1268916 at 150iterations 4.2920690E-03 7.0533276E-02 at 160iterations 2.5232863E-03 4.2441845E-02 at 170iterations 1.4905732E-03 2.3062587E-02 at 180iterations finished qdiffx linear iterations at : 08:56:10 total time elapsed so far: 15.53000 # loops : 180 mean,max change (kT/e) : 1.4905732E-03 2.3062587E-02 energy calculations done at 15.53000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.74000 DelPhi exited at 08:56:11 15.739u 0.308s 0:16.84 95.1% 0+0k 0+0io 0pf+0w