Tue Oct 11 08:06:22 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 08:06:22 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 = 3122 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: 0.5412144 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): -20.43000 43.21400 ymin,ymax (A): -2.101000 63.67700 zmin,zma (A): 3.344000 54.88500 x,y,z range (A): 63.64400 65.77800 51.54100 scale (grids/A): 0.5412144 object centre (A): 11.39200 30.78800 29.11450 number of atom coordinates read : 3122 total number of charged atoms : 2976 net assigned charge : 11.50002 assigned positive charge : 463.6107 centred at (gu) : 89.69480 90.57878 90.70150 assigned negative charge : -452.1120 centred at (gu) : 89.55371 90.61977 90.75436 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6200 nv = 96 ne = 84 npr = 57970 no. pairs analyzed = 57970 no. exposed pairs = 4406 no. arc points = 31984 no. surface atoms = 1478 nbur = 1644 mkacc time = 0.1700000 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 = 1.568000 m= 242 mr = 2887 m= 0 mr = 6 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3900000 number of dielectric boundary points 3549 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3176 ## 434 charges are in solution ## iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 7960 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 7.5500212E-10 3.5284406E-10 midg,1,midg; midg,igrid,midg 7.2079398E-10 4.2149795E-10 1,midg,midg; igrid,midg,midg -2.2965431E-10 1.2815121E-09 gauss-seidel spectral radius is 0.9824336 estimated iterations to convergence 62 setup time was (sec) 0.6600000 now iterating at: 08:06:23 rms-change max change #iterations 6.9991365E-02 11.33611 at 10iterations 4.4821328E-03 0.8018436 at 20iterations 2.9358294E-04 4.6341300E-02 at 30iterations 2.0287642E-05 3.0689240E-03 at 40iterations 1.7354029E-06 2.2888184E-04 at 50iterations finished qdiffx linear iterations at : 08:06:27 total time elapsed so far: 4.010000 # loops : 50 mean,max change (kT/e) : 1.7354029E-06 2.2888184E-04 energy calculations done at 4.010000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.200000 DelPhi exited at 08:06:28 4.202u 0.257s 0:05.16 86.2% 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 08:06:28 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 = 3122 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: 1.623643 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): -20.43000 43.21400 ymin,ymax (A): -2.101000 63.67700 zmin,zma (A): 3.344000 54.88500 x,y,z range (A): 63.64400 65.77800 51.54100 scale (grids/A): 1.623643 object centre (A): 11.39200 30.78800 29.11450 number of atom coordinates read : 3122 total number of charged atoms : 2976 net assigned charge : 11.50002 assigned positive charge : 463.6107 centred at (gu) : 89.08345 91.73528 92.10353 assigned negative charge : -452.1120 centred at (gu) : 88.66067 91.85911 92.26283 start vw surface at 0.1700000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 68288 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31984 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 19314 mr = 43043 m= 1836 mr = 12519 m= 54 mr = 764 m= 1 mr = 1 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 573 time to turn everything in is 0.6100000 number of dielectric boundary points 33166 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 428 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 22807 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) : 0.5412144 object centre at (A) : 11.39200 30.78800 29.11450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.9249892E-03 1.0435607E-02 midg,1,midg; midg,igrid,midg -6.2178667E-03 -1.0109441E-02 1,midg,midg; igrid,midg,midg 2.1176403E-03 2.5566058E-02 gauss-seidel spectral radius is 0.9981996 estimated iterations to convergence 187 setup time was (sec) 0.9100000 now iterating at: 08:06:29 rms-change max change #iterations 3.306302 153.2226 at 10iterations 1.373307 56.78130 at 20iterations 0.5707707 22.33953 at 30iterations 0.2380773 8.793274 at 40iterations 9.9082492E-02 3.832642 at 50iterations 4.1235801E-02 1.557289 at 60iterations 1.7197993E-02 0.6827011 at 70iterations 7.1995603E-03 0.2698879 at 80iterations 3.0007595E-03 0.1076040 at 90iterations 1.2492574E-03 4.6988964E-02 at 100iterations 5.2300352E-04 1.8371582E-02 at 110iterations 2.1888626E-04 8.0928802E-03 at 120iterations finished qdiffx linear iterations at : 08:06:37 total time elapsed so far: 9.370000 # loops : 120 mean,max change (kT/e) : 2.1888626E-04 8.0928802E-03 energy calculations done at 9.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.540000 DelPhi exited at 08:06:38 9.546u 0.319s 0:10.19 96.6% 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 Tue Oct 11 2011 at 08:06:38 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 = 3122 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: 2.435465 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): -20.43000 43.21400 ymin,ymax (A): -2.101000 63.67700 zmin,zma (A): 3.344000 54.88500 x,y,z range (A): 63.64400 65.77800 51.54100 scale (grids/A): 2.435465 object centre (A): 11.39200 30.78800 29.11450 number of atom coordinates read : 3122 total number of charged atoms : 2976 net assigned charge : 11.50002 assigned positive charge : 463.6107 centred at (gu) : 88.62491 92.60271 93.15498 assigned negative charge : -452.1120 centred at (gu) : 87.99099 92.78844 93.39420 start vw surface at 0.1900000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 158507 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31984 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 67557 mr = 106389 m= 17942 mr = 51415 m= 2625 mr = 12714 m= 175 mr = 1532 m= 2 mr = 69 m= 0 mr = 0 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 1824 time to turn everything in is 1.490000 number of dielectric boundary points 74689 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 30 iepsmp to db, and charging done at 1.640000 number of grid points assigned charge 23779 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) : 1.623643 object centre at (A) : 11.39200 30.78800 29.11450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 8.3615690E-02 0.1603603 midg,1,midg; midg,igrid,midg -0.1157575 -0.1053310 1,midg,midg; igrid,midg,midg 7.1706265E-02 0.3350327 gauss-seidel spectral radius is 0.9991548 estimated iterations to convergence 272 setup time was (sec) 1.810000 now iterating at: 08:06:40 rms-change max change #iterations 8.718830 274.7736 at 10iterations 4.984262 141.5851 at 20iterations 2.822295 69.25896 at 30iterations 1.589118 40.04313 at 40iterations 0.8919221 21.66557 at 50iterations 0.4953699 11.11401 at 60iterations 0.2761118 6.284219 at 70iterations 0.1531357 3.557751 at 80iterations 8.5036404E-02 1.799144 at 90iterations 4.7149613E-02 1.008051 at 100iterations 2.6116485E-02 0.5472050 at 110iterations 1.4415734E-02 0.3145924 at 120iterations 7.9676369E-03 0.1554742 at 130iterations 4.3985918E-03 9.9791527E-02 at 140iterations 2.4318278E-03 4.9247742E-02 at 150iterations 1.3413479E-03 2.5776863E-02 at 160iterations 7.4172945E-04 1.4545441E-02 at 170iterations 4.1016357E-04 8.3923340E-03 at 180iterations finished qdiffx linear iterations at : 08:06:54 total time elapsed so far: 15.72000 # loops : 180 mean,max change (kT/e) : 4.1016357E-04 8.3923340E-03 energy calculations done at 15.72000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.90000 DelPhi exited at 08:06:54 15.905u 0.307s 0:16.56 97.8% 0+0k 0+0io 0pf+0w