Wed Dec 28 11:01:40 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 11:01:40 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! 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: 0.6240578 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): -35.26500 10.55700 ymin,ymax (A): 0.6140000 41.47000 zmin,zma (A): -0.3370000 56.70900 x,y,z range (A): 45.82200 40.85600 57.04600 scale (grids/A): 0.6240578 object centre (A): -12.35400 21.04200 28.18600 number of atom coordinates read : 1966 total number of charged atoms : 1766 net assigned charge : -19.95203 assigned positive charge : 263.9204 centred at (gu) : 90.26366 89.75005 89.83544 assigned negative charge : -283.8723 centred at (gu) : 90.19611 89.84299 89.85126 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 5236 nv = 96 ne = 84 npr = 40237 no. pairs analyzed = 40237 no. exposed pairs = 2401 no. arc points = 16960 no. surface atoms = 813 nbur = 1153 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 263 mr = 2904 m= 3 mr = 39 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2400000 number of dielectric boundary points 2559 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1586 ## 122 charges are in solution ## iepsmp to db, and charging done at 0.3400000 number of grid points assigned charge 6030 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.7946379E-08 -1.8411278E-08 midg,1,midg; midg,igrid,midg -1.3866947E-08 -2.2119581E-08 1,midg,midg; igrid,midg,midg -2.0722435E-08 -1.5352786E-08 gauss-seidel spectral radius is 0.9866467 estimated iterations to convergence 71 setup time was (sec) 0.5100000 now iterating at: 11:01:41 rms-change max change #iterations 0.1140040 18.85683 at 10iterations 1.0609266E-02 1.807792 at 20iterations 9.9118124E-04 0.1984558 at 30iterations 9.2576636E-05 1.7737627E-02 at 40iterations 8.5534939E-06 1.2512207E-03 at 50iterations finished qdiffx linear iterations at : 11:01:45 total time elapsed so far: 4.200000 # loops : 50 mean,max change (kT/e) : 8.5534939E-06 1.2512207E-03 energy calculations done at 4.200000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.370000 DelPhi exited at 11:01:46 4.375u 0.395s 0:05.44 87.5% 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 11:01:46 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! 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: 1.872173 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): -35.26500 10.55700 ymin,ymax (A): 0.6140000 41.47000 zmin,zma (A): -0.3370000 56.70900 x,y,z range (A): 45.82200 40.85600 57.04600 scale (grids/A): 1.872173 object centre (A): -12.35400 21.04200 28.18600 number of atom coordinates read : 1966 total number of charged atoms : 1766 net assigned charge : -19.95203 assigned positive charge : 263.9204 centred at (gu) : 90.79127 89.25037 89.50636 assigned negative charge : -283.8723 centred at (gu) : 90.58860 89.52912 89.55409 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 56656 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16960 grid for indexing accessible points = 1.400000 m= 20986 mr = 39370 m= 3174 mr = 16025 m= 155 mr = 2011 m= 0 mr = 59 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4900000 number of dielectric boundary points 23506 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 72 iepsmp to db, and charging done at 0.6100000 number of grid points assigned charge 13918 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) : 0.6240578 object centre at (A) : -12.35400 21.04200 28.18600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.6421565E-02 -5.4328479E-02 midg,1,midg; midg,igrid,midg -2.2592654E-02 -3.0060114E-02 1,midg,midg; igrid,midg,midg -2.5053490E-02 -3.4157321E-02 gauss-seidel spectral radius is 0.9985133 estimated iterations to convergence 206 setup time was (sec) 0.8000000 now iterating at: 11:01:47 rms-change max change #iterations 3.412304 145.9377 at 10iterations 1.553741 67.24728 at 20iterations 0.7000992 25.82853 at 30iterations 0.3186899 11.75417 at 40iterations 0.1441208 5.037258 at 50iterations 6.5042131E-02 2.554772 at 60iterations 2.9532745E-02 1.131301 at 70iterations 1.3351919E-02 0.4803677 at 80iterations 6.0606338E-03 0.2157445 at 90iterations 2.7480267E-03 9.5975876E-02 at 100iterations 1.2452403E-03 4.5715332E-02 at 110iterations 5.6370511E-04 2.1893501E-02 at 120iterations finished qdiffx linear iterations at : 11:01:57 total time elapsed so far: 10.29000 # loops : 120 mean,max change (kT/e) : 5.6370511E-04 2.1893501E-02 energy calculations done at 10.29000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.46000 DelPhi exited at 11:01:58 10.462u 0.419s 0:12.33 88.1% 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 11:01:58 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: 256 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1966 !!! 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: 2.808260 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): -35.26500 10.55700 ymin,ymax (A): 0.6140000 41.47000 zmin,zma (A): -0.3370000 56.70900 x,y,z range (A): 45.82200 40.85600 57.04600 scale (grids/A): 2.808260 object centre (A): -12.35400 21.04200 28.18600 number of atom coordinates read : 1966 total number of charged atoms : 1766 net assigned charge : -19.95203 assigned positive charge : 263.9204 centred at (gu) : 91.18690 88.87553 89.25974 assigned negative charge : -283.8723 centred at (gu) : 90.88290 89.29366 89.33117 start vw surface at 0.1000000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 130703 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16960 grid for indexing accessible points = 1.400000 m= 67575 mr = 95043 m= 25053 mr = 56243 m= 5636 mr = 20784 m= 670 mr = 4224 m= 41 mr = 466 m= 0 mr = 17 time to grow re-entrant surface = 0.7600001 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.240000 number of dielectric boundary points 52901 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.370000 number of grid points assigned charge 14126 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) : 1.872173 object centre at (A) : -12.35400 21.04200 28.18600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6713467 -0.7955071 midg,1,midg; midg,igrid,midg -0.2494775 -0.3242731 1,midg,midg; igrid,midg,midg -0.2737831 -0.3731623 gauss-seidel spectral radius is 0.9992077 estimated iterations to convergence 280 setup time was (sec) 1.570000 now iterating at: 11:02:00 rms-change max change #iterations 8.170533 344.9208 at 10iterations 4.698374 113.5176 at 20iterations 2.669841 67.70441 at 30iterations 1.514673 33.83876 at 40iterations 0.8551814 23.94515 at 50iterations 0.4818485 10.37352 at 60iterations 0.2720510 6.528464 at 70iterations 0.1541653 3.181476 at 80iterations 8.6398236E-02 1.682457 at 90iterations 4.8725437E-02 1.014000 at 100iterations 2.7442459E-02 0.5877277 at 110iterations 1.5437846E-02 0.3279915 at 120iterations 8.6892303E-03 0.1828632 at 130iterations 4.8936438E-03 9.6775055E-02 at 140iterations 2.7522207E-03 5.8624268E-02 at 150iterations 1.5479184E-03 3.0798912E-02 at 160iterations 8.7041548E-04 2.0126343E-02 at 170iterations 4.9012993E-04 9.4451904E-03 at 180iterations finished qdiffx linear iterations at : 11:02:17 total time elapsed so far: 18.21000 # loops : 180 mean,max change (kT/e) : 4.9012993E-04 9.4451904E-03 energy calculations done at 18.21000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.38000 DelPhi exited at 11:02:19 18.389u 0.470s 0:20.91 90.1% 0+0k 0+0io 0pf+0w