Tue Nov 22 14:10:58 PST 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 Nov 22 2011 at 14:11:03 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6054113 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): 1.731000 44.49200 ymin,ymax (A): -24.29800 24.43900 zmin,zma (A): -29.16900 29.63400 x,y,z range (A): 42.76100 48.73700 58.80300 scale (grids/A): 0.6054113 object centre (A): 23.11150 7.0499420E-02 0.2325001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 90.22120 89.95002 89.88464 assigned negative charge : -284.8263 centred at (gu) : 90.40923 89.94837 89.87076 start vw surface at 0.1100000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 4901 nv = 96 ne = 84 npr = 39881 no. pairs analyzed = 39881 no. exposed pairs = 2439 no. arc points = 17222 no. surface atoms = 822 nbur = 1142 mkacc time = 8.0000006E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 235 mr = 2709 m= 3 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 20 time to turn everything in is 0.2200000 number of dielectric boundary points 2404 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1754 ## 177 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 5913 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1406275E-09 1.9416611E-09 midg,1,midg; midg,igrid,midg 1.5172419E-09 1.5876763E-09 1,midg,midg; igrid,midg,midg 7.0154478E-09 -4.7673283E-09 gauss-seidel spectral radius is 0.9858239 estimated iterations to convergence 69 setup time was (sec) 0.4400000 now iterating at: 14:11:06 rms-change max change #iterations 9.5539562E-02 17.24307 at 10iterations 8.1215631E-03 1.799786 at 20iterations 7.0084591E-04 0.1278286 at 30iterations 6.2048777E-05 1.0836601E-02 at 40iterations 5.3810495E-06 9.1171265E-04 at 50iterations finished qdiffx linear iterations at : 14:11:14 total time elapsed so far: 3.040000 # loops : 50 mean,max change (kT/e) : 5.3810495E-06 9.1171265E-04 energy calculations done at 3.040000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.220000 DelPhi exited at 14:11:18 3.221u 0.164s 0:16.41 20.5% 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 Tue Nov 22 2011 at 14:11:21 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.816234 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): 1.731000 44.49200 ymin,ymax (A): -24.29800 24.43900 zmin,zma (A): -29.16900 29.63400 x,y,z range (A): 42.76100 48.73700 58.80300 scale (grids/A): 1.816234 object centre (A): 23.11150 7.0499420E-02 0.2325001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 90.66367 89.85005 89.65364 assigned negative charge : -284.8263 centred at (gu) : 91.22782 89.84525 89.61260 start vw surface at 0.1100000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 52920 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17222 grid for indexing accessible points = 1.400000 m= 19093 mr = 36483 m= 2489 mr = 14480 m= 85 mr = 1462 m= 2 mr = 18 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 522 time to turn everything in is 0.3800000 number of dielectric boundary points 22146 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 156 iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 14296 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) : 0.6054113 object centre at (A) : 23.11150 7.0499420E-02 0.2325001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0294249E-02 2.3635501E-02 midg,1,midg; midg,igrid,midg -1.2347852E-03 -1.4677746E-03 1,midg,midg; igrid,midg,midg 1.0764806E-02 -1.4217295E-02 gauss-seidel spectral radius is 0.9984254 estimated iterations to convergence 200 setup time was (sec) 0.6300000 now iterating at: 14:11:25 rms-change max change #iterations 3.232774 143.3866 at 10iterations 1.428015 53.96549 at 20iterations 0.6341102 24.81182 at 30iterations 0.2806230 11.99051 at 40iterations 0.1241752 4.739028 at 50iterations 5.4921910E-02 2.281899 at 60iterations 2.4296235E-02 0.9347076 at 70iterations 1.0721492E-02 0.4067869 at 80iterations 4.7636130E-03 0.1791077 at 90iterations 2.1017173E-03 7.5425148E-02 at 100iterations 9.3078433E-04 3.3853590E-02 at 110iterations 4.1301694E-04 1.5602112E-02 at 120iterations finished qdiffx linear iterations at : 14:11:44 total time elapsed so far: 6.630000 # loops : 120 mean,max change (kT/e) : 4.1301694E-04 1.5602112E-02 energy calculations done at 6.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.810000 DelPhi exited at 14:11:47 6.813u 0.172s 0:27.29 25.5% 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 Tue Nov 22 2011 at 14:11:51 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 = 1964 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.724351 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): 1.731000 44.49200 ymin,ymax (A): -24.29800 24.43900 zmin,zma (A): -29.16900 29.63400 x,y,z range (A): 42.76100 48.73700 58.80300 scale (grids/A): 2.724351 object centre (A): 23.11150 7.0499420E-02 0.2325001 number of atom coordinates read : 1964 total number of charged atoms : 1832 net assigned charge : 3.000004 assigned positive charge : 287.8260 centred at (gu) : 90.99551 89.77503 89.48051 assigned negative charge : -284.8263 centred at (gu) : 91.84174 89.76802 89.41885 start vw surface at 0.1000000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 122095 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17222 grid for indexing accessible points = 1.400000 m= 62293 mr = 87945 m= 21917 mr = 51896 m= 4200 mr = 17917 m= 327 mr = 3078 m= 10 mr = 163 m= 0 mr = 0 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 1671 time to turn everything in is 0.9100000 number of dielectric boundary points 49843 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.030000 number of grid points assigned charge 14648 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) : 1.816234 object centre at (A) : 23.11150 7.0499420E-02 0.2325001 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1158209 0.1085229 midg,1,midg; midg,igrid,midg -5.4096729E-02 -4.9924817E-02 1,midg,midg; igrid,midg,midg 8.7912887E-02 -0.1870050 gauss-seidel spectral radius is 0.9991815 estimated iterations to convergence 276 setup time was (sec) 1.190000 now iterating at: 14:11:58 rms-change max change #iterations 7.743169 243.5796 at 10iterations 4.356440 139.3377 at 20iterations 2.434117 53.37045 at 30iterations 1.357164 35.63134 at 40iterations 0.7580655 16.37730 at 50iterations 0.4207524 9.209819 at 60iterations 0.2340391 4.906775 at 70iterations 0.1299272 2.802956 at 80iterations 7.2495401E-02 1.501851 at 90iterations 4.0366389E-02 0.8288002 at 100iterations 2.2436183E-02 0.5046515 at 110iterations 1.2519362E-02 0.2592821 at 120iterations 6.9510485E-03 0.1501212 at 130iterations 3.8667205E-03 8.6262703E-02 at 140iterations 2.1531261E-03 4.7473907E-02 at 150iterations 1.2004150E-03 2.6936531E-02 at 160iterations 6.6646939E-04 1.4636397E-02 at 170iterations 3.7181628E-04 9.9401474E-03 at 180iterations finished qdiffx linear iterations at : 14:12:28 total time elapsed so far: 10.52000 # loops : 180 mean,max change (kT/e) : 3.7181628E-04 9.9401474E-03 energy calculations done at 10.52000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.70000 DelPhi exited at 14:12:30 10.698u 0.153s 0:39.68 27.3% 0+0k 0+0io 0pf+0w