Wed Dec 28 11:01:59 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+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 Wed Dec 28 2011 at 11:01:59 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: 240 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 !!! 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 0.5787395 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): -25.66800 35.84500 ymin,ymax (A): -19.00900 20.51000 zmin,zma (A): -3.572000 38.47600 x,y,z range (A): 61.51300 39.51900 42.04800 scale (grids/A): 0.5787395 object centre (A): 5.088501 0.7505007 17.45200 number of atom coordinates read : 1964 total number of charged atoms : 1764 net assigned charge : -21.95202 assigned positive charge : 263.8745 centred at (gu) : 89.89463 90.27163 90.61832 assigned negative charge : -285.8263 centred at (gu) : 89.89960 90.38117 90.77247 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 4442 nv = 96 ne = 84 npr = 39977 no. pairs analyzed = 39977 no. exposed pairs = 2398 no. arc points = 17166 no. surface atoms = 810 nbur = 1154 mkacc time = 0.1000000 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= 176 mr = 2440 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 20 time to turn everything in is 0.2400000 number of dielectric boundary points 2170 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1667 ## 164 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 5346 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.1992632E-09 -7.7339397E-09 midg,1,midg; midg,igrid,midg -2.9208116E-09 -6.4686874E-09 1,midg,midg; igrid,midg,midg -4.6110396E-09 -4.5274007E-09 gauss-seidel spectral radius is 0.9845072 estimated iterations to convergence 66 setup time was (sec) 0.5700000 now iterating at: 11:02:00 rms-change max change #iterations 7.9396054E-02 15.70628 at 10iterations 6.2033446E-03 1.077691 at 20iterations 4.8332321E-04 9.0896606E-02 at 30iterations 3.7601385E-05 8.0718994E-03 at 40iterations 2.8638240E-06 5.2285194E-04 at 50iterations finished qdiffx linear iterations at : 11:02:07 total time elapsed so far: 7.030000 # loops : 50 mean,max change (kT/e) : 2.8638240E-06 5.2285194E-04 energy calculations done at 7.030000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.220000 DelPhi exited at 11:02:09 7.224u 0.506s 0:09.13 84.5% 0+0k 0+0io 6pf+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 11:02:09 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: 240 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 !!! 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 1.736218 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): -25.66800 35.84500 ymin,ymax (A): -19.00900 20.51000 zmin,zma (A): -3.572000 38.47600 x,y,z range (A): 61.51300 39.51900 42.04800 scale (grids/A): 1.736218 object centre (A): 5.088501 0.7505007 17.45200 number of atom coordinates read : 1964 total number of charged atoms : 1764 net assigned charge : -21.95202 assigned positive charge : 263.8745 centred at (gu) : 89.68443 90.81535 91.85526 assigned negative charge : -285.8263 centred at (gu) : 89.69897 91.14389 92.31750 start vw surface at 0.1000000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 48572 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17166 grid for indexing accessible points = 1.400000 m= 16339 mr = 33481 m= 1819 mr = 12239 m= 46 mr = 1038 m= 0 mr = 7 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 2269 time to turn everything in is 0.4000000 number of dielectric boundary points 20011 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 154 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 13751 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) : 0.5787395 object centre at (A) : 5.088501 0.7505007 17.45200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.5531588E-03 -2.7398154E-02 midg,1,midg; midg,igrid,midg -1.0640414E-02 -2.1814883E-02 1,midg,midg; igrid,midg,midg -2.1969510E-02 -2.9991020E-02 gauss-seidel spectral radius is 0.9982799 estimated iterations to convergence 191 setup time was (sec) 0.8000000 now iterating at: 11:02:10 rms-change max change #iterations 2.937487 149.5100 at 10iterations 1.249116 59.95750 at 20iterations 0.5351555 22.33819 at 30iterations 0.2279470 8.968346 at 40iterations 9.7271092E-02 4.644470 at 50iterations 4.1634552E-02 1.633715 at 60iterations 1.7722899E-02 0.7012186 at 70iterations 7.5303372E-03 0.2941179 at 80iterations 3.2173896E-03 0.1355324 at 90iterations 1.3731179E-03 5.2787781E-02 at 100iterations 5.8901665E-04 2.4108887E-02 at 110iterations 2.5033712E-04 9.5710754E-03 at 120iterations finished qdiffx linear iterations at : 11:02:28 total time elapsed so far: 18.85000 # loops : 120 mean,max change (kT/e) : 2.5033712E-04 9.5710754E-03 energy calculations done at 18.85000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.02000 DelPhi exited at 11:02:29 19.024u 0.661s 0:20.68 95.1% 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 Wed Dec 28 2011 at 11:02:29 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: 240 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1964 !!! 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= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.604327 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): -25.66800 35.84500 ymin,ymax (A): -19.00900 20.51000 zmin,zma (A): -3.572000 38.47600 x,y,z range (A): 61.51300 39.51900 42.04800 scale (grids/A): 2.604327 object centre (A): 5.088501 0.7505007 17.45200 number of atom coordinates read : 1964 total number of charged atoms : 1764 net assigned charge : -21.95202 assigned positive charge : 263.8745 centred at (gu) : 89.52670 91.22300 92.78296 assigned negative charge : -285.8263 centred at (gu) : 89.54855 91.71586 93.47631 start vw surface at 0.1000000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 112334 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17166 grid for indexing accessible points = 1.400000 m= 55436 mr = 80754 m= 17221 mr = 45751 m= 2831 mr = 14093 m= 164 mr = 2037 m= 2 mr = 103 m= 0 mr = 0 time to grow re-entrant surface = 0.5900000 no. cavity mid-points inaccessible to solvent = 8289 time to turn everything in is 1.010000 number of dielectric boundary points 45250 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.220000 number of grid points assigned charge 14110 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) : 1.736218 object centre at (A) : 5.088501 0.7505007 17.45200 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.8044324E-02 -0.3251720 midg,1,midg; midg,igrid,midg -0.1246266 -0.2624809 1,midg,midg; igrid,midg,midg -0.2452709 -0.3553782 gauss-seidel spectral radius is 0.9991345 estimated iterations to convergence 269 setup time was (sec) 1.550000 now iterating at: 11:02:32 rms-change max change #iterations 7.181121 232.6147 at 10iterations 3.963559 103.6259 at 20iterations 2.177650 52.99230 at 30iterations 1.195328 32.07552 at 40iterations 0.6569363 14.82834 at 50iterations 0.3588395 8.347300 at 60iterations 0.1970976 4.485493 at 70iterations 0.1077827 2.401290 at 80iterations 5.8939569E-02 1.385686 at 90iterations 3.2249704E-02 0.7375565 at 100iterations 1.7640395E-02 0.4856725 at 110iterations 9.6587390E-03 0.2254925 at 120iterations 5.2938857E-03 0.1212349 at 130iterations 2.8879270E-03 6.4207077E-02 at 140iterations 1.5883265E-03 3.5731316E-02 at 150iterations 8.6569606E-04 2.0216465E-02 at 160iterations 4.7377529E-04 1.0629654E-02 at 170iterations 2.5969019E-04 6.0911179E-03 at 180iterations finished qdiffx linear iterations at : 11:02:59 total time elapsed so far: 29.11000 # loops : 180 mean,max change (kT/e) : 2.5969019E-04 6.0911179E-03 energy calculations done at 29.11000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 29.28000 DelPhi exited at 11:03:01 29.289u 0.728s 0:31.52 95.1% 0+0k 0+0io 0pf+0w