Mon Oct 10 09:21:08 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 09:21:08 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6473316 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): -5.079000 35.40400 ymin,ymax (A): -3.943000 48.52600 zmin,zma (A): -24.37700 30.61800 x,y,z range (A): 40.48300 52.46900 54.99500 scale (grids/A): 0.6473316 object centre (A): 15.16250 22.29150 3.120501 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) : 90.43983 92.79097 90.29311 assigned negative charge : -284.8263 centred at (gu) : 90.56168 92.89940 90.21315 start vw surface at 0.1400000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 5647 nv = 96 ne = 84 npr = 40434 no. pairs analyzed = 40434 no. exposed pairs = 2376 no. arc points = 17226 no. surface atoms = 814 nbur = 1150 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 313 mr = 3178 m= 0 mr = 41 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 9 time to turn everything in is 0.2400000 number of dielectric boundary points 2741 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1729 ## 182 charges are in solution ## iepsmp to db, and charging done at 0.3500000 number of grid points assigned charge 6600 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4164839E-09 1.4815392E-08 midg,1,midg; midg,igrid,midg 9.3875050E-09 -1.0671682E-08 1,midg,midg; igrid,midg,midg 1.6540834E-08 -7.7465190E-09 gauss-seidel spectral radius is 0.9875787 estimated iterations to convergence 73 setup time was (sec) 0.4700000 now iterating at: 09:21:09 rms-change max change #iterations 0.1281674 20.73569 at 10iterations 1.2868476E-02 1.934359 at 20iterations 1.3052793E-03 0.2099953 at 30iterations 1.3238480E-04 2.0503998E-02 at 40iterations 1.3253308E-05 1.9645691E-03 at 50iterations finished qdiffx linear iterations at : 09:21:11 total time elapsed so far: 2.930000 # loops : 50 mean,max change (kT/e) : 1.3253308E-05 1.9645691E-03 energy calculations done at 2.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.110000 DelPhi exited at 09:21:12 3.118u 0.120s 0:03.60 89.7% 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 Mon Oct 10 2011 at 09:21:12 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.941995 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): -5.079000 35.40400 ymin,ymax (A): -3.943000 48.52600 zmin,zma (A): -24.37700 30.61800 x,y,z range (A): 40.48300 52.46900 54.99500 scale (grids/A): 1.941995 object centre (A): 15.16250 22.29150 3.120501 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) : 91.31982 98.37307 90.87933 assigned negative charge : -284.8263 centred at (gu) : 91.68529 98.69854 90.63959 start vw surface at 0.1300000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 60299 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17226 grid for indexing accessible points = 1.400000 m= 23064 mr = 41572 m= 3636 mr = 17857 m= 194 mr = 2364 m= 2 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 987 time to turn everything in is 0.4400000 number of dielectric boundary points 25323 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 113 iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 14453 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) : 0.6473316 object centre at (A) : 15.16250 22.29150 3.120501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3365244E-02 1.7021835E-02 midg,1,midg; midg,igrid,midg 3.0588802E-02 -5.2588223E-03 1,midg,midg; igrid,midg,midg 7.0976508E-03 -5.7327212E-03 gauss-seidel spectral radius is 0.9986094 estimated iterations to convergence 213 setup time was (sec) 0.6900000 now iterating at: 09:21:13 rms-change max change #iterations 3.650397 168.6581 at 10iterations 1.695652 62.96568 at 20iterations 0.7935923 29.43037 at 30iterations 0.3693118 13.41147 at 40iterations 0.1712058 5.651521 at 50iterations 7.9676487E-02 2.695845 at 60iterations 3.6945440E-02 1.307592 at 70iterations 1.7224923E-02 0.6184521 at 80iterations 7.9941982E-03 0.2903063 at 90iterations 3.6991877E-03 0.1463442 at 100iterations 1.7293677E-03 6.0675621E-02 at 110iterations 8.0351921E-04 2.6412964E-02 at 120iterations finished qdiffx linear iterations at : 09:21:19 total time elapsed so far: 6.630000 # loops : 120 mean,max change (kT/e) : 8.0351921E-04 2.6412964E-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 09:21:19 6.811u 0.169s 0:07.25 96.1% 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 Mon Oct 10 2011 at 09:21:19 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.912992 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): -5.079000 35.40400 ymin,ymax (A): -3.943000 48.52600 zmin,zma (A): -24.37700 30.61800 x,y,z range (A): 40.48300 52.46900 54.99500 scale (grids/A): 2.912992 object centre (A): 15.16250 22.29150 3.120501 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) : 91.97974 102.5596 91.31912 assigned negative charge : -284.8263 centred at (gu) : 92.52792 103.0480 90.95940 start vw surface at 0.1300000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 138750 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17226 grid for indexing accessible points = 1.400000 m= 72905 mr = 100014 m= 28472 mr = 60961 m= 6416 mr = 23886 m= 818 mr = 4884 m= 36 mr = 568 m= 0 mr = 8 time to grow re-entrant surface = 0.6000000 no. cavity mid-points inaccessible to solvent = 3401 time to turn everything in is 1.060000 number of dielectric boundary points 57076 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.180000 number of grid points assigned charge 14656 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) : 1.941995 object centre at (A) : 15.16250 22.29150 3.120501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.094129 5.9548587E-02 midg,1,midg; midg,igrid,midg 0.2942517 -8.8379346E-02 1,midg,midg; igrid,midg,midg 3.4531437E-02 -3.0421462E-02 gauss-seidel spectral radius is 0.9992378 estimated iterations to convergence 286 setup time was (sec) 1.340000 now iterating at: 09:21:21 rms-change max change #iterations 8.609743 458.4333 at 10iterations 4.939047 172.7412 at 20iterations 2.829201 58.14499 at 30iterations 1.610391 31.59595 at 40iterations 0.9210503 20.29575 at 50iterations 0.5249875 10.37635 at 60iterations 0.2988188 5.830803 at 70iterations 0.1695783 3.271811 at 80iterations 9.6725419E-02 1.960800 at 90iterations 5.4952625E-02 1.040581 at 100iterations 3.1286065E-02 0.6149178 at 110iterations 1.7832395E-02 0.3586006 at 120iterations 1.0103201E-02 0.2061157 at 130iterations 5.7531544E-03 0.1129398 at 140iterations 3.2788129E-03 6.3282490E-02 at 150iterations 1.8658586E-03 3.8528442E-02 at 160iterations 1.0601034E-03 2.0733833E-02 at 170iterations 6.0353370E-04 1.2611389E-02 at 180iterations finished qdiffx linear iterations at : 09:21:30 total time elapsed so far: 10.60000 # loops : 180 mean,max change (kT/e) : 6.0353370E-04 1.2611389E-02 energy calculations done at 10.60000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.79000 DelPhi exited at 09:21:31 10.789u 0.159s 0:11.22 97.4% 0+0k 0+0io 0pf+0w