Wed Dec 28 11:03:13 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 Wed Dec 28 2011 at 11:03:13 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5708055 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): -26.30500 36.06300 ymin,ymax (A): -19.15800 20.57000 zmin,zma (A): -3.393000 38.70400 x,y,z range (A): 62.36800 39.72800 42.09700 scale (grids/A): 0.5708055 object centre (A): 4.879000 0.7060003 17.65550 number of atom coordinates read : 1960 total number of charged atoms : 1760 net assigned charge : -21.95202 assigned positive charge : 267.0744 centred at (gu) : 90.03439 90.31897 90.49364 assigned negative charge : -289.0263 centred at (gu) : 90.04327 90.42290 90.64739 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 4285 nv = 96 ne = 84 npr = 39936 no. pairs analyzed = 39936 no. exposed pairs = 2474 no. arc points = 17454 no. surface atoms = 834 nbur = 1126 mkacc time = 0.1400000 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 = 1.512000 m= 174 mr = 2300 m= 0 mr = 11 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3000000 number of dielectric boundary points 2148 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1718 ## 172 charges are in solution ## iepsmp to db, and charging done at 0.5300000 number of grid points assigned charge 5255 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.6750520E-09 -5.7240515E-09 midg,1,midg; midg,igrid,midg -2.2101863E-09 -4.9102935E-09 1,midg,midg; igrid,midg,midg -3.3326994E-09 -3.5739243E-09 gauss-seidel spectral radius is 0.9840797 estimated iterations to convergence 65 setup time was (sec) 0.7900000 now iterating at: 11:03:15 rms-change max change #iterations 7.5681746E-02 13.55442 at 10iterations 5.6804633E-03 1.131490 at 20iterations 4.2256451E-04 7.8234196E-02 at 30iterations 3.1163429E-05 5.6686401E-03 at 40iterations 2.4257306E-06 4.4250488E-04 at 50iterations finished qdiffx linear iterations at : 11:03:21 total time elapsed so far: 7.310000 # loops : 50 mean,max change (kT/e) : 2.4257306E-06 4.4250488E-04 energy calculations done at 7.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.530000 DelPhi exited at 11:03:22 7.538u 0.708s 0:08.59 95.8% 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 Wed Dec 28 2011 at 11:03:22 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.712417 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): -26.30500 36.06300 ymin,ymax (A): -19.15800 20.57000 zmin,zma (A): -3.393000 38.70400 x,y,z range (A): 62.36800 39.72800 42.09700 scale (grids/A): 1.712417 object centre (A): 4.879000 0.7060003 17.65550 number of atom coordinates read : 1960 total number of charged atoms : 1760 net assigned charge : -21.95202 assigned positive charge : 267.0744 centred at (gu) : 90.10329 90.95705 91.48122 assigned negative charge : -289.0263 centred at (gu) : 90.12994 91.26904 91.94218 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 46800 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17454 grid for indexing accessible points = 1.400000 m= 15482 mr = 31753 m= 1497 mr = 11436 m= 30 mr = 790 m= 0 mr = 4 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 995 time to turn everything in is 0.5400000 number of dielectric boundary points 19826 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 145 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 13656 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) : 0.5708055 object centre at (A) : 4.879000 0.7060003 17.65550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.8346224E-03 -2.4712101E-02 midg,1,midg; midg,igrid,midg -9.3868002E-03 -1.9843390E-02 1,midg,midg; igrid,midg,midg -2.0598926E-02 -2.9538825E-02 gauss-seidel spectral radius is 0.9982334 estimated iterations to convergence 189 setup time was (sec) 1.020000 now iterating at: 11:03:24 rms-change max change #iterations 2.902353 194.6412 at 10iterations 1.217414 54.43301 at 20iterations 0.5115714 19.43242 at 30iterations 0.2158453 8.941684 at 40iterations 9.1227069E-02 3.862825 at 50iterations 3.8276266E-02 1.707670 at 60iterations 1.6253158E-02 0.6607780 at 70iterations 6.8459315E-03 0.3166161 at 80iterations 2.8808576E-03 0.1182098 at 90iterations 1.2163563E-03 5.1233292E-02 at 100iterations 5.1148707E-04 2.1926880E-02 at 110iterations 2.1640478E-04 9.0162754E-03 at 120iterations finished qdiffx linear iterations at : 11:03:38 total time elapsed so far: 15.57000 # loops : 120 mean,max change (kT/e) : 2.1640478E-04 9.0162754E-03 energy calculations done at 15.57000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.80000 DelPhi exited at 11:03:39 15.803u 0.758s 0:17.09 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 Wed Dec 28 2011 at 11:03:39 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: 263 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1960 !!! WARNING: GLN 2 has a net charge of -0.6880 !!! WARNING: GLN 7 has a net charge of -0.6880 !!! WARNING: ARG 8 has a net charge of -0.4460 !!! WARNING: GLN 18 has a net charge of -0.6880 !!! WARNING: ARG 41 has a net charge of -0.4460 !!! WARNING: ARG 57 has a net charge of -0.4460 !!! WARNING: GLN 58 has a net charge of -0.6880 !!! WARNING: GLN 61 has a net charge of -0.6880 !!! WARNING: ASN 83 has a net charge of -0.6880 !!! WARNING: ARG 87 has a net charge of -0.4460 !!! WARNING: ASN 88 has a net charge of -0.6880 !!! WARNING: GLN 92 has a net charge of -0.6880 !!! WARNING: ASN 98 has a net charge of -0.6880 !!! WARNING: GLN 101 has a net charge of -0.6880 !!! WARNING: GLN 106 has a net charge of -0.6880 !!! WARNING: ARG 107 has a net charge of -0.4460 !!! WARNING: GLN 117 has a net charge of -0.6880 !!! WARNING: ARG 140 has a net charge of -0.4460 !!! WARNING: ARG 156 has a net charge of -0.4460 !!! WARNING: GLN 157 has a net charge of -0.6880 !!! WARNING: GLN 160 has a net charge of -0.6880 !!! WARNING: ASN 182 has a net charge of -0.6880 !!! WARNING: ARG 186 has a net charge of -0.4460 !!! WARNING: ASN 187 has a net charge of -0.6880 !!! WARNING: GLN 191 has a net charge of -0.6880 !!! WARNING: ASN 197 has a net charge of -0.6880 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.568625 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): -26.30500 36.06300 ymin,ymax (A): -19.15800 20.57000 zmin,zma (A): -3.393000 38.70400 x,y,z range (A): 62.36800 39.72800 42.09700 scale (grids/A): 2.568625 object centre (A): 4.879000 0.7060003 17.65550 number of atom coordinates read : 1960 total number of charged atoms : 1760 net assigned charge : -21.95202 assigned positive charge : 267.0744 centred at (gu) : 90.15500 91.43560 92.22189 assigned negative charge : -289.0263 centred at (gu) : 90.19497 91.90355 92.91323 start vw surface at 0.1300000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 108198 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17454 grid for indexing accessible points = 1.400000 m= 52864 mr = 76914 m= 15801 mr = 43346 m= 2387 mr = 12667 m= 152 mr = 1646 m= 1 mr = 95 m= 0 mr = 0 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 3264 time to turn everything in is 1.300000 number of dielectric boundary points 44735 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.520000 number of grid points assigned charge 14070 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) : 1.712417 object centre at (A) : 4.879000 0.7060003 17.65550 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.2094413E-02 -0.2973840 midg,1,midg; midg,igrid,midg -0.1142763 -0.2483255 1,midg,midg; igrid,midg,midg -0.2371359 -0.4025907 gauss-seidel spectral radius is 0.9991208 estimated iterations to convergence 266 setup time was (sec) 1.860000 now iterating at: 11:03:42 rms-change max change #iterations 7.121981 296.6577 at 10iterations 3.915771 117.5010 at 20iterations 2.150700 61.98161 at 30iterations 1.176887 31.00303 at 40iterations 0.6409952 15.73774 at 50iterations 0.3492250 8.156723 at 60iterations 0.1900197 4.216500 at 70iterations 0.1035590 2.549372 at 80iterations 5.6238852E-02 1.367880 at 90iterations 3.0706353E-02 0.7164116 at 100iterations 1.6724151E-02 0.3799839 at 110iterations 9.1028679E-03 0.2305870 at 120iterations 4.9629235E-03 0.1236448 at 130iterations 2.7071028E-03 6.2967300E-02 at 140iterations 1.4683430E-03 3.6674172E-02 at 150iterations 8.0062699E-04 1.7444611E-02 at 160iterations 4.3578504E-04 1.0709763E-02 at 170iterations 2.3730526E-04 6.1187744E-03 at 180iterations finished qdiffx linear iterations at : 11:04:10 total time elapsed so far: 29.79000 # loops : 180 mean,max change (kT/e) : 2.3730526E-04 6.1187744E-03 energy calculations done at 29.79000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 30.03000 DelPhi exited at 11:04:10 30.030u 0.809s 0:31.24 98.6% 0+0k 0+0io 0pf+0w