Sun Oct 9 20:55:36 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 Sun Oct 9 2011 at 20:55:36 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2499 !!! WARNING: CYS 277 has a net charge of 0.5000 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: 0.6299101 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): -40.02100 16.49500 ymin,ymax (A): -11.99500 32.19500 zmin,zma (A): -17.16900 36.47400 x,y,z range (A): 56.51600 44.19000 53.64300 scale (grids/A): 0.6299101 object centre (A): -11.76300 10.10000 9.652499 number of atom coordinates read : 2499 total number of charged atoms : 2356 net assigned charge : 5.000005 assigned positive charge : 375.8490 centred at (gu) : 91.48002 88.93681 90.05110 assigned negative charge : -370.8497 centred at (gu) : 91.55359 88.89375 89.99245 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 6517 nv = 96 ne = 84 npr = 50949 no. pairs analyzed = 50949 no. exposed pairs = 3099 no. arc points = 22030 no. surface atoms = 1054 nbur = 1445 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 368 mr = 3491 m= 5 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 63 time to turn everything in is 0.3100000 number of dielectric boundary points 3355 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2268 ## 248 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8065 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.9120003E-10 1.0562067E-08 midg,1,midg; midg,igrid,midg 2.3439310E-09 7.2977842E-09 1,midg,midg; igrid,midg,midg 8.5109590E-09 -1.0767891E-09 gauss-seidel spectral radius is 0.9869373 estimated iterations to convergence 72 setup time was (sec) 0.5400000 now iterating at: 20:55:36 rms-change max change #iterations 0.1325545 23.25491 at 10iterations 1.2621276E-02 1.814159 at 20iterations 1.1977188E-03 0.1911399 at 30iterations 1.1521002E-04 1.5995026E-02 at 40iterations 1.0876654E-05 1.5869141E-03 at 50iterations finished qdiffx linear iterations at : 20:55:39 total time elapsed so far: 3.130000 # loops : 50 mean,max change (kT/e) : 1.0876654E-05 1.5869141E-03 energy calculations done at 3.130000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.320000 DelPhi exited at 20:55:39 3.321u 0.139s 0:03.80 90.7% 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 Sun Oct 9 2011 at 20:55:39 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 = 2499 !!! WARNING: CYS 277 has a net charge of 0.5000 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: 1.889730 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): -40.02100 16.49500 ymin,ymax (A): -11.99500 32.19500 zmin,zma (A): -17.16900 36.47400 x,y,z range (A): 56.51600 44.19000 53.64300 scale (grids/A): 1.889730 object centre (A): -11.76300 10.10000 9.652499 number of atom coordinates read : 2499 total number of charged atoms : 2356 net assigned charge : 5.000005 assigned positive charge : 375.8490 centred at (gu) : 94.43951 86.80978 90.15261 assigned negative charge : -370.8497 centred at (gu) : 94.66045 86.68122 89.97727 start vw surface at 0.1400000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 70338 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22030 grid for indexing accessible points = 1.400000 m= 23590 mr = 47667 m= 3741 mr = 16868 m= 274 mr = 2308 m= 2 mr = 118 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 1697 time to turn everything in is 0.5100000 number of dielectric boundary points 30984 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 172 iepsmp to db, and charging done at 0.6400000 number of grid points assigned charge 18498 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) : 0.6299101 object centre at (A) : -11.76300 10.10000 9.652499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6998088E-02 2.1527696E-02 midg,1,midg; midg,igrid,midg -1.4999965E-02 -1.1509315E-03 1,midg,midg; igrid,midg,midg 4.3741208E-02 -2.2834224E-04 gauss-seidel spectral radius is 0.9985983 estimated iterations to convergence 212 setup time was (sec) 0.8100000 now iterating at: 20:55:40 rms-change max change #iterations 4.043951 175.4192 at 10iterations 1.862769 67.62439 at 20iterations 0.8645182 28.40197 at 30iterations 0.4002355 12.01958 at 40iterations 0.1851422 6.963764 at 50iterations 8.5892819E-02 2.874567 at 60iterations 3.9639372E-02 1.373215 at 70iterations 1.8418454E-02 0.5883369 at 80iterations 8.5144266E-03 0.3192239 at 90iterations 3.9486615E-03 0.1237946 at 100iterations 1.8244038E-03 6.1156273E-02 at 110iterations 8.4867637E-04 2.7179718E-02 at 120iterations finished qdiffx linear iterations at : 20:55:47 total time elapsed so far: 7.400000 # loops : 120 mean,max change (kT/e) : 8.4867637E-04 2.7179718E-02 energy calculations done at 7.400000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.580000 DelPhi exited at 20:55:48 7.586u 0.181s 0:08.11 95.6% 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 Sun Oct 9 2011 at 20:55:48 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 = 2499 !!! WARNING: CYS 277 has a net charge of 0.5000 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: 2.834596 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): -40.02100 16.49500 ymin,ymax (A): -11.99500 32.19500 zmin,zma (A): -17.16900 36.47400 x,y,z range (A): 56.51600 44.19000 53.64300 scale (grids/A): 2.834596 object centre (A): -11.76300 10.10000 9.652499 number of atom coordinates read : 2499 total number of charged atoms : 2356 net assigned charge : 5.000005 assigned positive charge : 375.8490 centred at (gu) : 96.65926 85.21455 90.22872 assigned negative charge : -370.8497 centred at (gu) : 96.99073 85.02185 89.96578 start vw surface at 0.1500000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 162924 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22030 grid for indexing accessible points = 1.400000 m= 77508 mr = 115892 m= 26659 mr = 62328 m= 6641 mr = 20997 m= 1194 mr = 4998 m= 87 mr = 853 m= 0 mr = 37 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 5528 time to turn everything in is 1.280000 number of dielectric boundary points 69908 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 18846 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) : 1.889730 object centre at (A) : -11.76300 10.10000 9.652499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2692343 0.1999673 midg,1,midg; midg,igrid,midg -0.1225274 -3.8709052E-02 1,midg,midg; igrid,midg,midg 0.4731624 -0.1094252 gauss-seidel spectral radius is 0.9992468 estimated iterations to convergence 288 setup time was (sec) 1.580000 now iterating at: 20:55:49 rms-change max change #iterations 9.478188 339.4617 at 10iterations 5.467247 121.5428 at 20iterations 3.135924 60.87905 at 30iterations 1.793449 38.30758 at 40iterations 1.024997 19.01816 at 50iterations 0.5863503 11.95203 at 60iterations 0.3353540 6.163254 at 70iterations 0.1912094 3.380935 at 80iterations 0.1091685 2.118124 at 90iterations 6.2227875E-02 1.131973 at 100iterations 3.5611417E-02 0.6608057 at 110iterations 2.0283129E-02 0.4016323 at 120iterations 1.1577994E-02 0.2445297 at 130iterations 6.6183587E-03 0.1249785 at 140iterations 3.7767503E-03 7.3215485E-02 at 150iterations 2.1512159E-03 3.9737225E-02 at 160iterations 1.2285983E-03 2.1737576E-02 at 170iterations 7.0276792E-04 1.2401342E-02 at 180iterations finished qdiffx linear iterations at : 20:55:59 total time elapsed so far: 11.57000 # loops : 180 mean,max change (kT/e) : 7.0276792E-04 1.2401342E-02 energy calculations done at 11.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.75000 DelPhi exited at 20:56:00 11.755u 0.184s 0:12.21 97.7% 0+0k 0+0io 0pf+0w