Sat Oct 8 23:12:24 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 Sat Oct 8 2011 at 23:12:25 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2443 !!! WARNING: HIT 84 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.6590273 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): -28.29100 25.40300 ymin,ymax (A): -15.37400 27.78100 zmin,zma (A): -5.948000 48.07100 x,y,z range (A): 53.69400 43.15500 54.01900 scale (grids/A): 0.6590273 object centre (A): -1.444000 6.203500 21.06150 number of atom coordinates read : 2443 total number of charged atoms : 2307 net assigned charge : 11.01402 assigned positive charge : 360.9941 centred at (gu) : 90.69588 89.34599 88.68759 assigned negative charge : -349.9809 centred at (gu) : 90.68738 89.43357 88.69189 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7233 nv = 96 ne = 84 npr = 49019 no. pairs analyzed = 49019 no. exposed pairs = 3332 no. arc points = 23690 no. surface atoms = 1104 nbur = 1339 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 467 mr = 3657 m= 6 mr = 56 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3993 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2287 ## 199 charges are in solution ## iepsmp to db, and charging done at 0.3800000 number of grid points assigned charge 8471 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.6299831E-08 2.0278399E-08 midg,1,midg; midg,igrid,midg 4.8212030E-08 1.0393180E-08 1,midg,midg; igrid,midg,midg 2.2282139E-08 3.2864889E-08 gauss-seidel spectral radius is 0.9880610 estimated iterations to convergence 75 setup time was (sec) 0.4900000 now iterating at: 23:12:25 rms-change max change #iterations 0.1589349 24.52223 at 10iterations 1.6566576E-02 2.465403 at 20iterations 1.8218013E-03 0.2696648 at 30iterations 2.4254026E-04 3.8530350E-02 at 40iterations 4.8886530E-05 7.3661804E-03 at 50iterations finished qdiffx linear iterations at : 23:12:28 total time elapsed so far: 2.940000 # loops : 50 mean,max change (kT/e) : 4.8886530E-05 7.3661804E-03 energy calculations done at 2.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 23:12:28 3.127u 0.156s 0:03.61 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 Sat Oct 8 2011 at 23:12:28 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2443 !!! WARNING: HIT 84 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: 1.977082 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): -28.29100 25.40300 ymin,ymax (A): -15.37400 27.78100 zmin,zma (A): -5.948000 48.07100 x,y,z range (A): 53.69400 43.15500 54.01900 scale (grids/A): 1.977082 object centre (A): -1.444000 6.203500 21.06150 number of atom coordinates read : 2443 total number of charged atoms : 2307 net assigned charge : 11.01402 assigned positive charge : 360.9941 centred at (gu) : 92.08746 88.03781 86.06215 assigned negative charge : -349.9809 centred at (gu) : 92.06206 88.30048 86.07568 start vw surface at 0.1500000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 76390 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23690 grid for indexing accessible points = 1.400000 m= 28571 mr = 50571 m= 5375 mr = 20109 m= 381 mr = 3242 m= 8 mr = 150 m= 0 mr = 0 time to grow re-entrant surface = 0.2600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5500000 number of dielectric boundary points 36653 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 106 iepsmp to db, and charging done at 0.6600000 number of grid points assigned charge 18209 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) : 0.6590273 object centre at (A) : -1.444000 6.203500 21.06150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.3358930E-02 4.6283737E-02 midg,1,midg; midg,igrid,midg 3.3237413E-02 3.3897411E-03 1,midg,midg; igrid,midg,midg 2.4901008E-02 6.3712418E-02 gauss-seidel spectral radius is 0.9987263 estimated iterations to convergence 222 setup time was (sec) 0.8100000 now iterating at: 23:12:29 rms-change max change #iterations 4.327216 236.2249 at 10iterations 2.078284 73.43115 at 20iterations 0.9940117 32.56108 at 30iterations 0.4782092 15.10397 at 40iterations 0.2280792 7.751360 at 50iterations 0.1088737 3.505081 at 60iterations 5.2631341E-02 1.599068 at 70iterations 2.5266979E-02 0.8166876 at 80iterations 1.2127082E-02 0.3698273 at 90iterations 5.8409730E-03 0.1809826 at 100iterations 2.8137669E-03 8.9437485E-02 at 110iterations 1.3559721E-03 4.5768738E-02 at 120iterations finished qdiffx linear iterations at : 23:12:35 total time elapsed so far: 6.910000 # loops : 120 mean,max change (kT/e) : 1.3559721E-03 4.5768738E-02 energy calculations done at 6.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.090000 DelPhi exited at 23:12:36 7.089u 0.162s 0:07.61 95.1% 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 Sat Oct 8 2011 at 23:12:36 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: 295 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2443 !!! WARNING: HIT 84 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.965623 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): -28.29100 25.40300 ymin,ymax (A): -15.37400 27.78100 zmin,zma (A): -5.948000 48.07100 x,y,z range (A): 53.69400 43.15500 54.01900 scale (grids/A): 2.965623 object centre (A): -1.444000 6.203500 21.06150 number of atom coordinates read : 2443 total number of charged atoms : 2307 net assigned charge : 11.01402 assigned positive charge : 360.9941 centred at (gu) : 93.13107 87.05651 84.09309 assigned negative charge : -349.9809 centred at (gu) : 93.09306 87.45076 84.11340 start vw surface at 0.1500000 fill in re-entrant regions at 0.4600000 boundary points on vw surface= 176180 reading accessible surface arcs data from file ARCDAT no. of arc points read = 23690 grid for indexing accessible points = 1.400000 m= 88843 mr = 123143 m= 35035 mr = 70345 m= 9892 mr = 27322 m= 1731 mr = 7168 m= 125 mr = 1147 m= 3 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.8200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.390000 number of dielectric boundary points 82645 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.510000 number of grid points assigned charge 18455 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) : 1.977082 object centre at (A) : -1.444000 6.203500 21.06150 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2453548 0.6275831 midg,1,midg; midg,igrid,midg 0.3001082 -6.3962708E-03 1,midg,midg; igrid,midg,midg 0.2261432 0.4924321 gauss-seidel spectral radius is 0.9992955 estimated iterations to convergence 297 setup time was (sec) 1.670000 now iterating at: 23:12:38 rms-change max change #iterations 10.30253 377.6591 at 10iterations 6.206526 153.1429 at 20iterations 3.692458 94.62451 at 30iterations 2.187031 43.31378 at 40iterations 1.294032 28.27219 at 50iterations 0.7642591 14.96143 at 60iterations 0.4488292 8.943573 at 70iterations 0.2635566 5.059429 at 80iterations 0.1543052 3.062459 at 90iterations 9.0639636E-02 1.744286 at 100iterations 5.2928351E-02 1.042244 at 110iterations 3.0998543E-02 0.5204029 at 120iterations 1.8106302E-02 0.3443918 at 130iterations 1.0571210E-02 0.1929283 at 140iterations 6.1809067E-03 0.1102337 at 150iterations 3.6176851E-03 6.6358566E-02 at 160iterations 2.1267822E-03 3.9631844E-02 at 170iterations 1.2530702E-03 2.2728443E-02 at 180iterations finished qdiffx linear iterations at : 23:12:47 total time elapsed so far: 11.42000 # loops : 180 mean,max change (kT/e) : 1.2530702E-03 2.2728443E-02 energy calculations done at 11.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.59000 DelPhi exited at 23:12:48 11.592u 0.186s 0:12.07 97.5% 0+0k 0+0io 0pf+0w