Sun Oct 9 00:36:08 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 Sun Oct 9 2011 at 00:36:08 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 = 2322 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6442156 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): -26.96800 27.37900 ymin,ymax (A): 44.44100 86.17700 zmin,zma (A): -12.78700 42.47400 x,y,z range (A): 54.34700 41.73600 55.26100 scale (grids/A): 0.6442156 object centre (A): 0.2054996 65.30901 14.84350 number of atom coordinates read : 2322 total number of charged atoms : 2188 net assigned charge : 11.00002 assigned positive charge : 336.1696 centred at (gu) : 90.47048 91.09792 91.41979 assigned negative charge : -325.1702 centred at (gu) : 90.43831 91.01349 91.41161 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.0000000E-02 boundary points on vw surface= 6753 nv = 96 ne = 84 npr = 46062 no. pairs analyzed = 46062 no. exposed pairs = 3073 no. arc points = 21911 no. surface atoms = 1027 nbur = 1295 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 399 mr = 3568 m= 1 mr = 50 m= 0 mr = 0 time to grow re-entrant surface = 8.0000013E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1700000 number of dielectric boundary points 3535 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2088 ## 194 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 7814 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2718430E-08 2.5169907E-08 midg,1,midg; midg,igrid,midg 6.9336665E-09 3.4011048E-08 1,midg,midg; igrid,midg,midg 1.3033890E-08 2.3549005E-08 gauss-seidel spectral radius is 0.9875011 estimated iterations to convergence 73 setup time was (sec) 0.3600000 now iterating at: 00:36:09 rms-change max change #iterations 0.1382393 21.10302 at 10iterations 1.3737195E-02 2.088720 at 20iterations 1.4453698E-03 0.1891408 at 30iterations 1.7402215E-04 2.5741577E-02 at 40iterations 2.9325762E-05 4.6901703E-03 at 50iterations finished qdiffx linear iterations at : 00:36:12 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 2.9325762E-05 4.6901703E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 00:36:12 3.383u 0.199s 0:03.85 92.7% 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 Sun Oct 9 2011 at 00:36:12 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 = 2322 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.932647 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): -26.96800 27.37900 ymin,ymax (A): 44.44100 86.17700 zmin,zma (A): -12.78700 42.47400 x,y,z range (A): 54.34700 41.73600 55.26100 scale (grids/A): 1.932647 object centre (A): 0.2054996 65.30901 14.84350 number of atom coordinates read : 2322 total number of charged atoms : 2188 net assigned charge : 11.00002 assigned positive charge : 336.1696 centred at (gu) : 91.41129 93.29383 94.25912 assigned negative charge : -325.1702 centred at (gu) : 91.31480 93.04055 94.23476 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 71619 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21911 grid for indexing accessible points = 1.400000 m= 26386 mr = 48255 m= 4307 mr = 19128 m= 258 mr = 2596 m= 4 mr = 93 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 352 time to turn everything in is 0.3700000 number of dielectric boundary points 32502 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 139 iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 17252 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) : 0.6442156 object centre at (A) : 0.2054996 65.30901 14.84350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 6.4455882E-02 4.5164298E-02 midg,1,midg; midg,igrid,midg -3.4552652E-03 2.9781386E-02 1,midg,midg; igrid,midg,midg 4.2185068E-02 5.6053985E-02 gauss-seidel spectral radius is 0.9986559 estimated iterations to convergence 216 setup time was (sec) 0.5900000 now iterating at: 00:36:13 rms-change max change #iterations 3.968065 175.5892 at 10iterations 1.871970 78.77692 at 20iterations 0.8798713 28.18013 at 30iterations 0.4130169 12.77760 at 40iterations 0.1943802 6.284833 at 50iterations 9.1528364E-02 3.269202 at 60iterations 4.3098211E-02 1.411309 at 70iterations 2.0290775E-02 0.6368933 at 80iterations 9.5608355E-03 0.3449402 at 90iterations 4.5395535E-03 0.1346135 at 100iterations 2.1421204E-03 6.7700386E-02 at 110iterations 1.0245278E-03 3.4671783E-02 at 120iterations finished qdiffx linear iterations at : 00:36:20 total time elapsed so far: 7.730000 # loops : 120 mean,max change (kT/e) : 1.0245278E-03 3.4671783E-02 energy calculations done at 7.730000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.870000 DelPhi exited at 00:36:21 7.872u 0.187s 0:08.50 94.7% 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 Sun Oct 9 2011 at 00:36:21 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 = 2322 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.898970 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): -26.96800 27.37900 ymin,ymax (A): 44.44100 86.17700 zmin,zma (A): -12.78700 42.47400 x,y,z range (A): 54.34700 41.73600 55.26100 scale (grids/A): 2.898970 object centre (A): 0.2054996 65.30901 14.84350 number of atom coordinates read : 2322 total number of charged atoms : 2188 net assigned charge : 11.00002 assigned positive charge : 336.1696 centred at (gu) : 92.11698 94.94075 96.38865 assigned negative charge : -325.1702 centred at (gu) : 91.97230 94.56084 96.35218 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 165060 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21911 grid for indexing accessible points = 1.400000 m= 84002 mr = 116818 m= 31491 mr = 67920 m= 7860 mr = 25048 m= 1149 mr = 5782 m= 68 mr = 749 m= 0 mr = 26 time to grow re-entrant surface = 0.5300000 no. cavity mid-points inaccessible to solvent = 1215 time to turn everything in is 0.9200000 number of dielectric boundary points 73287 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.010000 number of grid points assigned charge 17500 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) : 1.932647 object centre at (A) : 0.2054996 65.30901 14.84350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.055300 0.5161446 midg,1,midg; midg,igrid,midg -3.4425814E-02 0.2963957 1,midg,midg; igrid,midg,midg 0.5104058 0.5999711 gauss-seidel spectral radius is 0.9992698 estimated iterations to convergence 292 setup time was (sec) 1.150000 now iterating at: 00:36:22 rms-change max change #iterations 9.408126 346.8190 at 10iterations 5.555889 131.5081 at 20iterations 3.262497 69.67844 at 30iterations 1.900913 38.33334 at 40iterations 1.109495 24.30009 at 50iterations 0.6444439 13.58624 at 60iterations 0.3748845 7.889214 at 70iterations 0.2177465 4.170805 at 80iterations 0.1263392 2.494022 at 90iterations 7.3151238E-02 1.488197 at 100iterations 4.2337943E-02 0.8464584 at 110iterations 2.4466783E-02 0.4699099 at 120iterations 1.4163041E-02 0.2736340 at 130iterations 8.1785079E-03 0.1687298 at 140iterations 4.7349427E-03 0.1010857 at 150iterations 2.7456104E-03 5.3240299E-02 at 160iterations 1.5933231E-03 2.9127121E-02 at 170iterations 9.2502631E-04 1.9536972E-02 at 180iterations finished qdiffx linear iterations at : 00:36:33 total time elapsed so far: 12.30000 # loops : 180 mean,max change (kT/e) : 9.2502631E-04 1.9536972E-02 energy calculations done at 12.30000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.43000 DelPhi exited at 00:36:34 12.434u 0.204s 0:12.96 97.4% 0+0k 0+0io 0pf+0w