Tue Oct 11 06:13:59 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 06:13:59 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 = 2046 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: 0.7041278 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): 16.38800 63.51200 ymin,ymax (A): -3.490000 32.93500 zmin,zma (A): 21.90500 72.46400 x,y,z range (A): 47.12400 36.42500 50.55901 scale (grids/A): 0.7041278 object centre (A): 39.95000 14.72250 47.18450 number of atom coordinates read : 2046 total number of charged atoms : 1917 net assigned charge : 5.500006 assigned positive charge : 308.7220 centred at (gu) : 90.85698 89.92776 89.05542 assigned negative charge : -303.2222 centred at (gu) : 90.95708 89.99390 89.02214 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6898 nv = 96 ne = 84 npr = 41298 no. pairs analyzed = 41298 no. exposed pairs = 2461 no. arc points = 17005 no. surface atoms = 839 nbur = 1207 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 466 mr = 3948 m= 5 mr = 113 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2800000 number of dielectric boundary points 3308 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1559 ## 131 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 7639 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.3972313E-08 4.8615409E-08 midg,1,midg; midg,igrid,midg 7.3730916E-08 1.3611362E-08 1,midg,midg; igrid,midg,midg 7.4191988E-08 -2.4448210E-09 gauss-seidel spectral radius is 0.9894846 estimated iterations to convergence 79 setup time was (sec) 0.5000000 now iterating at: 06:13:59 rms-change max change #iterations 0.1922794 26.14055 at 10iterations 2.4044838E-02 3.754440 at 20iterations 2.9809873E-03 0.3899822 at 30iterations 4.4355902E-04 5.6209564E-02 at 40iterations 9.4429961E-05 1.3173103E-02 at 50iterations finished qdiffx linear iterations at : 06:14:02 total time elapsed so far: 3.140000 # loops : 50 mean,max change (kT/e) : 9.4429961E-05 1.3173103E-02 energy calculations done at 3.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.330000 DelPhi exited at 06:14:03 3.333u 0.153s 0:03.82 91.0% 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 06:14:03 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2046 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: 2.112383 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): 16.38800 63.51200 ymin,ymax (A): -3.490000 32.93500 zmin,zma (A): 21.90500 72.46400 x,y,z range (A): 47.12400 36.42500 50.55901 scale (grids/A): 2.112383 object centre (A): 39.95000 14.72250 47.18450 number of atom coordinates read : 2046 total number of charged atoms : 1917 net assigned charge : 5.500006 assigned positive charge : 308.7220 centred at (gu) : 92.57098 89.78326 87.16619 assigned negative charge : -303.2222 centred at (gu) : 92.87138 89.98183 87.06634 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 73249 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17005 grid for indexing accessible points = 1.400000 m= 29994 mr = 52032 m= 6121 mr = 22989 m= 611 mr = 4173 m= 16 mr = 323 m= 0 mr = 4 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5900000 number of dielectric boundary points 30470 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 59 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 15189 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) : 0.7041278 object centre at (A) : 39.95000 14.72250 47.18450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1371739E-02 3.4913201E-02 midg,1,midg; midg,igrid,midg 2.3955995E-02 6.6078915E-03 1,midg,midg; igrid,midg,midg 2.7211709E-02 2.5153209E-02 gauss-seidel spectral radius is 0.9988173 estimated iterations to convergence 230 setup time was (sec) 0.9000000 now iterating at: 06:14:04 rms-change max change #iterations 4.493124 181.5002 at 10iterations 2.224469 77.61090 at 20iterations 1.096486 34.60686 at 30iterations 0.5417098 16.87316 at 40iterations 0.2678895 8.206970 at 50iterations 0.1324849 4.024307 at 60iterations 6.5668158E-02 2.037869 at 70iterations 3.2450110E-02 1.049583 at 80iterations 1.6172320E-02 0.5313740 at 90iterations 8.0449888E-03 0.2501473 at 100iterations 4.0106904E-03 0.1352124 at 110iterations 2.0306280E-03 6.1798096E-02 at 120iterations finished qdiffx linear iterations at : 06:14:11 total time elapsed so far: 7.960000 # loops : 120 mean,max change (kT/e) : 2.0306280E-03 6.1798096E-02 energy calculations done at 7.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.150000 DelPhi exited at 06:14:11 8.149u 0.281s 0:08.75 96.2% 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 Tue Oct 11 2011 at 06:14:11 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 = 2046 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: 3.168575 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): 16.38800 63.51200 ymin,ymax (A): -3.490000 32.93500 zmin,zma (A): 21.90500 72.46400 x,y,z range (A): 47.12400 36.42500 50.55901 scale (grids/A): 3.168575 object centre (A): 39.95000 14.72250 47.18450 number of atom coordinates read : 2046 total number of charged atoms : 1917 net assigned charge : 5.500006 assigned positive charge : 308.7220 centred at (gu) : 93.85651 89.67490 85.74930 assigned negative charge : -303.2222 centred at (gu) : 94.30704 89.97279 85.59952 start vw surface at 0.1300000 fill in re-entrant regions at 0.8200000 boundary points on vw surface= 168713 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17005 grid for indexing accessible points = 1.400000 m= 92928 mr = 125270 m= 38897 mr = 77673 m= 11603 mr = 32254 m= 2376 mr = 9122 m= 283 mr = 1761 m= 9 mr = 171 m= 0 mr = 4 time to grow re-entrant surface = 0.9100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.840000 number of dielectric boundary points 68554 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.990000 number of grid points assigned charge 15332 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) : 2.112383 object centre at (A) : 39.95000 14.72250 47.18450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2542431 6.9735415E-02 midg,1,midg; midg,igrid,midg 0.1989339 5.0445765E-02 1,midg,midg; igrid,midg,midg 0.2779917 0.4506285 gauss-seidel spectral radius is 0.9992932 estimated iterations to convergence 297 setup time was (sec) 2.180000 now iterating at: 06:14:14 rms-change max change #iterations 10.00398 328.3248 at 10iterations 5.903406 120.7813 at 20iterations 3.480770 79.15382 at 30iterations 2.046632 41.75055 at 40iterations 1.199546 22.92864 at 50iterations 0.7043197 12.96056 at 60iterations 0.4131225 7.835236 at 70iterations 0.2413805 4.742701 at 80iterations 0.1414909 2.623253 at 90iterations 8.2795016E-02 1.473705 at 100iterations 4.8434079E-02 0.8769922 at 110iterations 2.8415767E-02 0.5146110 at 120iterations 1.6705107E-02 0.3087664 at 130iterations 9.8874085E-03 0.2071953 at 140iterations 5.9486772E-03 0.1110702 at 150iterations 3.6574726E-03 7.5149536E-02 at 160iterations 2.3379277E-03 4.1351318E-02 at 170iterations 1.5749373E-03 2.9725790E-02 at 180iterations finished qdiffx linear iterations at : 06:14:25 total time elapsed so far: 13.38000 # loops : 180 mean,max change (kT/e) : 1.5749373E-03 2.9725790E-02 energy calculations done at 13.38000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.57000 DelPhi exited at 06:14:26 13.572u 0.275s 0:14.37 96.3% 0+0k 0+0io 0pf+0w