Mon Oct 10 10:24:46 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 Mon Oct 10 2011 at 10:24:46 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 = 2769 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5652768 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): -20.10400 42.87400 ymin,ymax (A): -9.075000 45.52100 zmin,zma (A): -1.639000 51.51000 x,y,z range (A): 62.97800 54.59600 53.14900 scale (grids/A): 0.5652768 object centre (A): 11.38500 18.22300 24.93550 number of atom coordinates read : 2769 total number of charged atoms : 2621 net assigned charge : 8.000016 assigned positive charge : 403.1321 centred at (gu) : 91.03513 90.43009 86.55005 assigned negative charge : -395.1325 centred at (gu) : 91.19908 90.41888 86.46312 start vw surface at 0.1000000 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 5882 nv = 96 ne = 84 npr = 53645 no. pairs analyzed = 53645 no. exposed pairs = 4219 no. arc points = 30488 no. surface atoms = 1401 nbur = 1368 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.512000 m= 277 mr = 2563 m= 1 mr = 5 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2100000 number of dielectric boundary points 3592 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2975 ## 340 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 7566 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.4314683E-11 9.3100511E-10 midg,1,midg; midg,igrid,midg 8.5976709E-10 1.3390012E-09 1,midg,midg; igrid,midg,midg 2.3067512E-09 -1.1353720E-09 gauss-seidel spectral radius is 0.9838535 estimated iterations to convergence 65 setup time was (sec) 0.4100000 now iterating at: 10:24:47 rms-change max change #iterations 8.2722776E-02 15.29941 at 10iterations 5.9511648E-03 1.060364 at 20iterations 4.7338661E-04 9.2529297E-02 at 30iterations 5.7725741E-05 1.2804031E-02 at 40iterations 1.1862132E-05 3.0002594E-03 at 50iterations finished qdiffx linear iterations at : 10:24:50 total time elapsed so far: 3.320000 # loops : 50 mean,max change (kT/e) : 1.1862132E-05 3.0002594E-03 energy calculations done at 3.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 10:24:50 3.481u 0.175s 0:04.04 90.3% 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 Mon Oct 10 2011 at 10:24:50 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 = 2769 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.695830 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): -20.10400 42.87400 ymin,ymax (A): -9.075000 45.52100 zmin,zma (A): -1.639000 51.51000 x,y,z range (A): 62.97800 54.59600 53.14900 scale (grids/A): 1.695830 object centre (A): 11.38500 18.22300 24.93550 number of atom coordinates read : 2769 total number of charged atoms : 2621 net assigned charge : 8.000016 assigned positive charge : 403.1321 centred at (gu) : 93.10511 91.28984 79.64968 assigned negative charge : -395.1325 centred at (gu) : 93.59717 91.25630 79.38906 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 63594 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30488 grid for indexing accessible points = 1.400000 m= 19650 mr = 38592 m= 2237 mr = 12444 m= 74 mr = 957 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 33560 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 276 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 20253 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) : 0.5652768 object centre at (A) : 11.38500 18.22300 24.93550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.7522418E-04 5.7389447E-03 midg,1,midg; midg,igrid,midg 1.5638947E-02 1.3088363E-02 1,midg,midg; igrid,midg,midg 1.3464467E-02 -1.6985368E-02 gauss-seidel spectral radius is 0.9983141 estimated iterations to convergence 193 setup time was (sec) 0.5600000 now iterating at: 10:24:51 rms-change max change #iterations 3.383766 158.1469 at 10iterations 1.447288 65.74044 at 20iterations 0.6199551 26.01621 at 30iterations 0.2649325 9.861476 at 40iterations 0.1134046 4.130120 at 50iterations 4.8787814E-02 1.824663 at 60iterations 2.0904170E-02 0.7829819 at 70iterations 8.9877071E-03 0.3203917 at 80iterations 3.8639437E-03 0.1481037 at 90iterations 1.6584080E-03 6.1225891E-02 at 100iterations 7.1985752E-04 2.5951385E-02 at 110iterations 3.1277546E-04 1.1998177E-02 at 120iterations finished qdiffx linear iterations at : 10:24:58 total time elapsed so far: 7.690000 # loops : 120 mean,max change (kT/e) : 3.1277546E-04 1.1998177E-02 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.840000 DelPhi exited at 10:24:59 7.841u 0.223s 0:08.44 95.4% 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 Mon Oct 10 2011 at 10:24:59 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 = 2769 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.543746 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): -20.10400 42.87400 ymin,ymax (A): -9.075000 45.52100 zmin,zma (A): -1.639000 51.51000 x,y,z range (A): 62.97800 54.59600 53.14900 scale (grids/A): 2.543746 object centre (A): 11.38500 18.22300 24.93550 number of atom coordinates read : 2769 total number of charged atoms : 2621 net assigned charge : 8.000016 assigned positive charge : 403.1321 centred at (gu) : 94.65770 91.93481 74.47443 assigned negative charge : -395.1325 centred at (gu) : 95.39571 91.88440 74.08340 start vw surface at 0.1100000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 146934 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30488 grid for indexing accessible points = 1.400000 m= 65494 mr = 95352 m= 19825 mr = 48657 m= 3373 mr = 13936 m= 279 mr = 2084 m= 7 mr = 87 m= 0 mr = 1 time to grow re-entrant surface = 0.4500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.8400000 number of dielectric boundary points 75795 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 0.9400000 number of grid points assigned charge 20955 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) : 1.695830 object centre at (A) : 11.38500 18.22300 24.93550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.7797890E-03 6.3548967E-02 midg,1,midg; midg,igrid,midg 0.2701201 0.1725578 1,midg,midg; igrid,midg,midg 0.1021603 -0.6173971 gauss-seidel spectral radius is 0.9991845 estimated iterations to convergence 277 setup time was (sec) 1.090000 now iterating at: 10:25:00 rms-change max change #iterations 8.895318 352.7245 at 10iterations 5.205444 156.2441 at 20iterations 2.998332 82.56385 at 30iterations 1.717286 44.17046 at 40iterations 0.9756418 25.46306 at 50iterations 0.5522323 13.16664 at 60iterations 0.3115914 7.667241 at 70iterations 0.1755712 4.359344 at 80iterations 9.8602630E-02 2.335077 at 90iterations 5.5442661E-02 1.303551 at 100iterations 3.1085312E-02 0.7993078 at 110iterations 1.7402612E-02 0.3872833 at 120iterations 9.7452039E-03 0.2196155 at 130iterations 5.4443968E-03 0.1201668 at 140iterations 3.0476123E-03 7.4861526E-02 at 150iterations 1.7060940E-03 3.5774231E-02 at 160iterations 9.4927510E-04 2.1949768E-02 at 170iterations 5.3319376E-04 1.1951447E-02 at 180iterations finished qdiffx linear iterations at : 10:25:12 total time elapsed so far: 12.43000 # loops : 180 mean,max change (kT/e) : 5.3319376E-04 1.1951447E-02 energy calculations done at 12.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.57000 DelPhi exited at 10:25:13 12.572u 1.020s 0:13.96 97.3% 0+0k 0+0io 0pf+0w