Tue Oct 11 07:57:37 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 07:57:37 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 = 2483 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: 0.6120519 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): -6.690000 51.47500 ymin,ymax (A): -22.34900 22.86500 zmin,zma (A): 8.762000 54.28900 x,y,z range (A): 58.16500 45.21400 45.52700 scale (grids/A): 0.6120519 object centre (A): 22.39250 0.2579994 31.52550 number of atom coordinates read : 2483 total number of charged atoms : 2346 net assigned charge : 8.500010 assigned positive charge : 377.6051 centred at (gu) : 89.94272 90.01312 89.95077 assigned negative charge : -369.1056 centred at (gu) : 90.02702 89.99690 89.77608 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6033 nv = 96 ne = 84 npr = 50504 no. pairs analyzed = 50504 no. exposed pairs = 2946 no. arc points = 20650 no. surface atoms = 994 nbur = 1489 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 276 mr = 3328 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 2959 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2118 ## 232 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 7531 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.6016206E-09 1.3792801E-08 midg,1,midg; midg,igrid,midg 4.5402584E-09 6.1952599E-09 1,midg,midg; igrid,midg,midg 9.6705959E-09 1.0930266E-09 gauss-seidel spectral radius is 0.9861642 estimated iterations to convergence 70 setup time was (sec) 0.6400000 now iterating at: 07:57:38 rms-change max change #iterations 0.1167792 21.91655 at 10iterations 1.0633050E-02 1.793083 at 20iterations 1.0289828E-03 0.1589413 at 30iterations 1.0755431E-04 1.8127441E-02 at 40iterations 1.2963880E-05 2.1171570E-03 at 50iterations finished qdiffx linear iterations at : 07:57:41 total time elapsed so far: 3.840000 # loops : 50 mean,max change (kT/e) : 1.2963880E-05 2.1171570E-03 energy calculations done at 3.840000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.080000 DelPhi exited at 07:57:42 4.084u 0.184s 0:04.60 92.6% 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 07:57:42 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 = 2483 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 1.836156 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): -6.690000 51.47500 ymin,ymax (A): -22.34900 22.86500 zmin,zma (A): 8.762000 54.28900 x,y,z range (A): 58.16500 45.21400 45.52700 scale (grids/A): 1.836156 object centre (A): 22.39250 0.2579994 31.52550 number of atom coordinates read : 2483 total number of charged atoms : 2346 net assigned charge : 8.500010 assigned positive charge : 377.6051 centred at (gu) : 89.82800 90.03922 89.85201 assigned negative charge : -369.1056 centred at (gu) : 90.08075 89.99054 89.32813 start vw surface at 0.1800000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 66010 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20650 grid for indexing accessible points = 1.400000 m= 22454 mr = 46066 m= 2844 mr = 16450 m= 110 mr = 1618 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 0.2700000 no. cavity mid-points inaccessible to solvent = 563 time to turn everything in is 0.6100000 number of dielectric boundary points 27259 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 168 iepsmp to db, and charging done at 0.7700000 number of grid points assigned charge 18324 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) : 0.6120519 object centre at (A) : 22.39250 0.2579994 31.52550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.5122809E-03 3.8341224E-02 midg,1,midg; midg,igrid,midg 1.0238521E-03 6.8086237E-03 1,midg,midg; igrid,midg,midg 3.1699158E-02 3.4755826E-02 gauss-seidel spectral radius is 0.9985162 estimated iterations to convergence 206 setup time was (sec) 0.9600000 now iterating at: 07:57:43 rms-change max change #iterations 3.820980 184.8710 at 10iterations 1.734496 70.92091 at 20iterations 0.7865581 26.14095 at 30iterations 0.3577435 13.35637 at 40iterations 0.1623579 5.287394 at 50iterations 7.3662952E-02 2.447418 at 60iterations 3.3409972E-02 1.218993 at 70iterations 1.5240790E-02 0.5310249 at 80iterations 6.9071567E-03 0.2567787 at 90iterations 3.1420293E-03 0.1083221 at 100iterations 1.4317301E-03 4.9196720E-02 at 110iterations 6.4961833E-04 2.4085045E-02 at 120iterations finished qdiffx linear iterations at : 07:57:51 total time elapsed so far: 8.940000 # loops : 120 mean,max change (kT/e) : 6.4961833E-04 2.4085045E-02 energy calculations done at 8.940000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.180000 DelPhi exited at 07:57:52 9.180u 0.238s 0:09.72 96.8% 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 07:57:52 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 = 2483 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.754234 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): -6.690000 51.47500 ymin,ymax (A): -22.34900 22.86500 zmin,zma (A): 8.762000 54.28900 x,y,z range (A): 58.16500 45.21400 45.52700 scale (grids/A): 2.754234 object centre (A): 22.39250 0.2579994 31.52550 number of atom coordinates read : 2483 total number of charged atoms : 2346 net assigned charge : 8.500010 assigned positive charge : 377.6051 centred at (gu) : 89.74197 90.05867 89.77795 assigned negative charge : -369.1056 centred at (gu) : 90.12112 89.98589 88.99200 start vw surface at 0.2000000 fill in re-entrant regions at 0.5400000 boundary points on vw surface= 152813 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20650 grid for indexing accessible points = 1.400000 m= 75061 mr = 111477 m= 24307 mr = 61770 m= 4791 mr = 19125 m= 554 mr = 3437 m= 25 mr = 308 m= 0 mr = 13 time to grow re-entrant surface = 0.8600000 no. cavity mid-points inaccessible to solvent = 1973 time to turn everything in is 1.510000 number of dielectric boundary points 61421 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.680000 number of grid points assigned charge 18760 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) : 1.836156 object centre at (A) : 22.39250 0.2579994 31.52550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1266745 0.4395504 midg,1,midg; midg,igrid,midg -7.9906816E-03 2.7449753E-02 1,midg,midg; igrid,midg,midg 0.1759140 0.1855448 gauss-seidel spectral radius is 0.9992173 estimated iterations to convergence 282 setup time was (sec) 1.890000 now iterating at: 07:57:54 rms-change max change #iterations 8.999267 416.8325 at 10iterations 5.141513 125.0270 at 20iterations 2.917881 75.84743 at 30iterations 1.655654 37.38404 at 40iterations 0.9350295 20.03408 at 50iterations 0.5297844 11.16453 at 60iterations 0.3002384 6.047441 at 70iterations 0.1698197 3.746658 at 80iterations 9.6043624E-02 1.918335 at 90iterations 5.4179601E-02 1.128359 at 100iterations 3.0612767E-02 0.6040916 at 110iterations 1.7330242E-02 0.3354092 at 120iterations 9.7805317E-03 0.1883316 at 130iterations 5.5365297E-03 0.1063919 at 140iterations 3.1300234E-03 5.7782173E-02 at 150iterations 1.7685129E-03 3.4015656E-02 at 160iterations 1.0043993E-03 1.9618988E-02 at 170iterations 5.7169661E-04 1.0886669E-02 at 180iterations finished qdiffx linear iterations at : 07:58:07 total time elapsed so far: 14.58000 # loops : 180 mean,max change (kT/e) : 5.7169661E-04 1.0886669E-02 energy calculations done at 14.58000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.82000 DelPhi exited at 07:58:07 14.824u 0.245s 0:15.36 98.0% 0+0k 0+0io 0pf+0w