Tue Nov 22 14:12:06 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+sph2.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 = amb2.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 14:12:11 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6369541 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): -5.176000 35.07500 ymin,ymax (A): -3.724000 48.43800 zmin,zma (A): -24.40200 31.48900 x,y,z range (A): 40.25100 52.16200 55.89100 scale (grids/A): 0.6369541 object centre (A): 14.94950 22.35700 3.543500 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 292.9999 centred at (gu) : 90.52337 92.55344 90.08888 assigned negative charge : -290.0002 centred at (gu) : 90.63860 92.69231 90.03011 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 5491 nv = 96 ne = 84 npr = 40167 no. pairs analyzed = 40167 no. exposed pairs = 2502 no. arc points = 17641 no. surface atoms = 850 nbur = 1120 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 294 mr = 3067 m= 2 mr = 32 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.1600000 number of dielectric boundary points 2688 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1738 ## 162 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 6432 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.3929254E-10 9.1670431E-09 midg,1,midg; midg,igrid,midg 8.8473611E-09 -1.2337244E-08 1,midg,midg; igrid,midg,midg 1.1972966E-08 -5.5539493E-09 gauss-seidel spectral radius is 0.9871764 estimated iterations to convergence 72 setup time was (sec) 0.3800000 now iterating at: 14:12:15 rms-change max change #iterations 0.1242484 19.12235 at 10iterations 1.2085291E-02 1.771214 at 20iterations 1.1771424E-03 0.2043686 at 30iterations 1.1446649E-04 1.6895294E-02 at 40iterations 1.0976583E-05 1.6279221E-03 at 50iterations finished qdiffx linear iterations at : 14:12:25 total time elapsed so far: 3.600000 # loops : 50 mean,max change (kT/e) : 1.0976583E-05 1.6279221E-03 energy calculations done at 3.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.740000 DelPhi exited at 14:12:26 3.745u 0.227s 0:15.61 25.3% 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 Tue Nov 22 2011 at 14:12:28 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.910862 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): -5.176000 35.07500 ymin,ymax (A): -3.724000 48.43800 zmin,zma (A): -24.40200 31.48900 x,y,z range (A): 40.25100 52.16200 55.89100 scale (grids/A): 1.910862 object centre (A): 14.94950 22.35700 3.543500 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 292.9999 centred at (gu) : 91.57022 97.66021 90.26653 assigned negative charge : -290.0002 centred at (gu) : 91.91600 98.07703 90.09053 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 58920 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17641 grid for indexing accessible points = 1.400000 m= 21794 mr = 40554 m= 3124 mr = 16610 m= 133 mr = 1981 m= 2 mr = 43 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 1397 time to turn everything in is 0.3300000 number of dielectric boundary points 24785 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 119 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 14467 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) : 0.6369541 object centre at (A) : 14.94950 22.35700 3.543500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.3328803E-02 1.4081473E-02 midg,1,midg; midg,igrid,midg 3.2747705E-02 -8.5934363E-03 1,midg,midg; igrid,midg,midg 8.1454096E-03 -5.3190673E-03 gauss-seidel spectral radius is 0.9985673 estimated iterations to convergence 209 setup time was (sec) 0.5900000 now iterating at: 14:12:33 rms-change max change #iterations 3.647371 174.5542 at 10iterations 1.674697 65.13430 at 20iterations 0.7728294 28.19363 at 30iterations 0.3556514 12.98769 at 40iterations 0.1626665 5.461589 at 50iterations 7.4580289E-02 3.063287 at 60iterations 3.4353629E-02 1.214880 at 70iterations 1.5751580E-02 0.5891132 at 80iterations 7.2965645E-03 0.2688550 at 90iterations 3.3292032E-03 0.1247940 at 100iterations 1.5324581E-03 5.1794052E-02 at 110iterations 7.0253009E-04 2.7404785E-02 at 120iterations finished qdiffx linear iterations at : 14:12:57 total time elapsed so far: 8.740000 # loops : 120 mean,max change (kT/e) : 7.0253009E-04 2.7404785E-02 energy calculations done at 8.740000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.870000 DelPhi exited at 14:12:59 8.868u 0.256s 0:31.23 29.1% 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 Tue Nov 22 2011 at 14:13:01 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.866293 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): -5.176000 35.07500 ymin,ymax (A): -3.724000 48.43800 zmin,zma (A): -24.40200 31.48900 x,y,z range (A): 40.25100 52.16200 55.89100 scale (grids/A): 2.866293 object centre (A): 14.94950 22.35700 3.543500 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 292.9999 centred at (gu) : 92.35528 101.4902 90.39980 assigned negative charge : -290.0002 centred at (gu) : 92.87414 102.1155 90.13578 start vw surface at 5.9999999E-02 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 135984 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17641 grid for indexing accessible points = 1.400000 m= 70091 mr = 97936 m= 25641 mr = 58371 m= 5741 mr = 21106 m= 710 mr = 4417 m= 35 mr = 468 m= 0 mr = 11 time to grow re-entrant surface = 0.4400000 no. cavity mid-points inaccessible to solvent = 4993 time to turn everything in is 0.8100000 number of dielectric boundary points 55893 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9200000 number of grid points assigned charge 14700 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) : 1.910862 object centre at (A) : 14.94950 22.35700 3.543500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.087559 4.2420227E-02 midg,1,midg; midg,igrid,midg 0.3589490 -0.1571032 1,midg,midg; igrid,midg,midg 5.3673793E-02 -3.0792542E-02 gauss-seidel spectral radius is 0.9992256 estimated iterations to convergence 284 setup time was (sec) 1.100000 now iterating at: 14:13:07 rms-change max change #iterations 8.651335 450.8418 at 10iterations 4.978094 151.9615 at 20iterations 2.836394 74.89503 at 30iterations 1.616221 38.47202 at 40iterations 0.9175992 21.66336 at 50iterations 0.5220765 11.47888 at 60iterations 0.2958087 6.724060 at 70iterations 0.1680714 3.664663 at 80iterations 9.5014416E-02 1.878124 at 90iterations 5.3777128E-02 1.034922 at 100iterations 3.0487491E-02 0.6660004 at 110iterations 1.7278263E-02 0.3720169 at 120iterations 9.7913900E-03 0.2133408 at 130iterations 5.5504018E-03 0.1206207 at 140iterations 3.1455166E-03 6.2301636E-02 at 150iterations 1.7755450E-03 3.5420895E-02 at 160iterations 1.0057869E-03 2.2148132E-02 at 170iterations 5.7120412E-04 1.0728955E-02 at 180iterations finished qdiffx linear iterations at : 14:13:47 total time elapsed so far: 14.42000 # loops : 180 mean,max change (kT/e) : 5.7120412E-04 1.0728955E-02 energy calculations done at 14.42000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.56000 DelPhi exited at 14:13:53 14.564u 0.289s 0:52.21 28.4% 0+0k 0+0io 0pf+0w