Sun Oct 9 02:16:56 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 Sun Oct 9 2011 at 02:16:56 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2032 !!! WARNING: MG2 213 has a net charge of 1.4000 !!! WARNING: SAM 214 has a net charge of -0.6000 !!! WARNING: SAM 1 has a net charge of -0.5000 !!! WARNING: SAM 3 has a net charge of 0.4200 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: 0.7477577 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): -36.07800 4.293000 ymin,ymax (A): -7.608000 40.00100 zmin,zma (A): -4.911000 38.54700 x,y,z range (A): 40.37100 47.60900 43.45800 scale (grids/A): 0.7477577 object centre (A): -15.89250 16.19650 16.81800 number of atom coordinates read : 2032 total number of charged atoms : 1923 net assigned charge : -5.279992 assigned positive charge : 306.3568 centred at (gu) : 88.94859 90.37329 89.36858 assigned negative charge : -311.6371 centred at (gu) : 89.02480 90.33574 89.33643 start vw surface at 7.9999998E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 8124 nv = 96 ne = 84 npr = 41252 no. pairs analyzed = 41252 no. exposed pairs = 2408 no. arc points = 16675 no. surface atoms = 826 nbur = 1206 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 694 mr = 4974 m= 8 mr = 222 m= 0 mr = 0 time to grow re-entrant surface = 8.0000013E-02 no. cavity mid-points inaccessible to solvent = 56 time to turn everything in is 0.1700000 number of dielectric boundary points 3630 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1182 ## 85 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 8262 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6598592E-07 -6.6064786E-08 midg,1,midg; midg,igrid,midg -1.4413648E-07 -7.1890454E-08 1,midg,midg; igrid,midg,midg -2.6744097E-08 -1.6457362E-07 gauss-seidel spectral radius is 0.9906688 estimated iterations to convergence 84 setup time was (sec) 0.3700000 now iterating at: 02:16:56 rms-change max change #iterations 0.2559913 36.72784 at 10iterations 3.5625231E-02 4.734335 at 20iterations 4.8574121E-03 0.6596546 at 30iterations 7.2112889E-04 8.4213257E-02 at 40iterations 1.1380137E-04 1.7710686E-02 at 50iterations finished qdiffx linear iterations at : 02:16:59 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 1.1380137E-04 1.7710686E-02 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.350000 DelPhi exited at 02:16:59 3.355u 0.164s 0:03.82 91.8% 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 Sun Oct 9 2011 at 02:16:59 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2032 !!! WARNING: MG2 213 has a net charge of 1.4000 !!! WARNING: SAM 214 has a net charge of -0.6000 !!! WARNING: SAM 1 has a net charge of -0.5000 !!! WARNING: SAM 3 has a net charge of 0.4200 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: 2.243273 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): -36.07800 4.293000 ymin,ymax (A): -7.608000 40.00100 zmin,zma (A): -4.911000 38.54700 x,y,z range (A): 40.37100 47.60900 43.45800 scale (grids/A): 2.243273 object centre (A): -15.89250 16.19650 16.81800 number of atom coordinates read : 2032 total number of charged atoms : 1923 net assigned charge : -5.279992 assigned positive charge : 306.3568 centred at (gu) : 86.84543 91.11974 88.10558 assigned negative charge : -311.6371 centred at (gu) : 87.07416 91.00735 88.00922 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 84653 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16675 grid for indexing accessible points = 1.400000 m= 37902 mr = 61792 m= 10268 mr = 30161 m= 1416 mr = 8019 m= 75 mr = 975 m= 1 mr = 15 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 1632 time to turn everything in is 0.4300000 number of dielectric boundary points 33353 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 17 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 15334 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) : 0.7477577 object centre at (A) : -15.89250 16.19650 16.81800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.6106561E-02 6.3989223E-03 midg,1,midg; midg,igrid,midg -1.2199566E-02 2.6261002E-02 1,midg,midg; igrid,midg,midg -1.9396378E-02 -5.2557085E-02 gauss-seidel spectral radius is 0.9989324 estimated iterations to convergence 242 setup time was (sec) 0.6600000 now iterating at: 02:17:00 rms-change max change #iterations 5.095920 260.9601 at 10iterations 2.601706 80.74976 at 20iterations 1.336375 41.05600 at 30iterations 0.6842826 18.81189 at 40iterations 0.3512397 10.61746 at 50iterations 0.1797681 5.627247 at 60iterations 9.2121303E-02 2.392311 at 70iterations 4.7325894E-02 1.457912 at 80iterations 2.4237145E-02 0.6775551 at 90iterations 1.2483884E-02 0.3799462 at 100iterations 6.3953660E-03 0.1826086 at 110iterations 3.3022608E-03 9.5081329E-02 at 120iterations finished qdiffx linear iterations at : 02:17:08 total time elapsed so far: 7.920000 # loops : 120 mean,max change (kT/e) : 3.3022608E-03 9.5081329E-02 energy calculations done at 7.920000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.060000 DelPhi exited at 02:17:08 8.061u 0.209s 0:08.53 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 Sun Oct 9 2011 at 02:17:08 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2032 !!! WARNING: MG2 213 has a net charge of 1.4000 !!! WARNING: SAM 214 has a net charge of -0.6000 !!! WARNING: SAM 1 has a net charge of -0.5000 !!! WARNING: SAM 3 has a net charge of 0.4200 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: 3.364910 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): -36.07800 4.293000 ymin,ymax (A): -7.608000 40.00100 zmin,zma (A): -4.911000 38.54700 x,y,z range (A): 40.37100 47.60900 43.45800 scale (grids/A): 3.364910 object centre (A): -15.89250 16.19650 16.81800 number of atom coordinates read : 2032 total number of charged atoms : 1923 net assigned charge : -5.279992 assigned positive charge : 306.3568 centred at (gu) : 85.26814 91.67959 87.15823 assigned negative charge : -311.6371 centred at (gu) : 85.61134 91.51107 87.01385 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 194750 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16675 grid for indexing accessible points = 1.400000 m= 112246 mr = 147378 m= 54082 mr = 95884 m= 20794 mr = 46795 m= 5865 mr = 17863 m= 1001 mr = 4889 m= 85 mr = 810 m= 2 mr = 45 m= 0 mr = 0 time to grow re-entrant surface = 0.7200000 no. cavity mid-points inaccessible to solvent = 5214 time to turn everything in is 1.320000 number of dielectric boundary points 75161 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.410000 number of grid points assigned charge 15384 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) : 2.243273 object centre at (A) : -15.89250 16.19650 16.81800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1693204 0.2310845 midg,1,midg; midg,igrid,midg -0.2139570 0.4404570 1,midg,midg; igrid,midg,midg 3.8372579E-03 -0.3414727 gauss-seidel spectral radius is 0.9993170 estimated iterations to convergence 302 setup time was (sec) 1.560000 now iterating at: 02:17:10 rms-change max change #iterations 10.95267 300.1812 at 10iterations 6.478179 125.2136 at 20iterations 3.823215 68.70800 at 30iterations 2.251852 40.27489 at 40iterations 1.328403 22.61879 at 50iterations 0.7811520 12.53963 at 60iterations 0.4602502 7.793130 at 70iterations 0.2712560 4.242290 at 80iterations 0.1591845 2.365420 at 90iterations 9.3691379E-02 1.717615 at 100iterations 5.5215701E-02 0.9252224 at 110iterations 3.2575749E-02 0.4928082 at 120iterations 1.9221617E-02 0.3120679 at 130iterations 1.1403676E-02 0.1848946 at 140iterations 6.8234936E-03 0.1174607 at 150iterations 4.1406252E-03 6.9383621E-02 at 160iterations 2.5910761E-03 4.7377586E-02 at 170iterations 1.6813286E-03 3.3683777E-02 at 180iterations finished qdiffx linear iterations at : 02:17:21 total time elapsed so far: 12.90000 # loops : 180 mean,max change (kT/e) : 1.6813286E-03 3.3683777E-02 energy calculations done at 12.90000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.03000 DelPhi exited at 02:17:21 13.037u 0.211s 0:13.51 98.0% 0+0k 0+0io 0pf+0w