Mon Oct 10 17:08:57 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 Mon Oct 10 2011 at 17:08:57 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 = 2894 !!! WARNING: GLY 31 has a net charge of 0.5000 !!! WARNING: ALA 172 has a net charge of 0.5000 !!! WARNING: PRO 352 has a net charge of 0.5000 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: 0.5438934 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): -34.40800 31.04600 ymin,ymax (A): -22.57000 25.10500 zmin,zma (A): -37.95900 6.852000 x,y,z range (A): 65.45400 47.67500 44.81100 scale (grids/A): 0.5438934 object centre (A): -1.681001 1.267500 -15.55350 number of atom coordinates read : 2894 total number of charged atoms : 2754 net assigned charge : 0.5000146 assigned positive charge : 431.5321 centred at (gu) : 89.72030 90.34534 90.22995 assigned negative charge : -431.0332 centred at (gu) : 89.71899 90.18829 90.33117 start vw surface at 7.9999998E-02 fill in re-entrant regions at 9.0000004E-02 boundary points on vw surface= 5528 nv = 96 ne = 84 npr = 58139 no. pairs analyzed = 58139 no. exposed pairs = 3830 no. arc points = 26861 no. surface atoms = 1293 nbur = 1601 mkacc time = 9.0000004E-02 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 = 1.596000 m= 229 mr = 2735 m= 0 mr = 10 time to grow re-entrant surface = 0.1000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2000000 number of dielectric boundary points 3012 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2704 ## 336 charges are in solution ## iepsmp to db, and charging done at 0.2600000 number of grid points assigned charge 7266 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 5.8852240E-10 -6.1860700E-10 midg,1,midg; midg,igrid,midg -8.4998047E-10 1.0320979E-09 1,midg,midg; igrid,midg,midg 2.1335834E-11 3.3193615E-11 gauss-seidel spectral radius is 0.9825704 estimated iterations to convergence 62 setup time was (sec) 0.3900000 now iterating at: 17:08:57 rms-change max change #iterations 6.7317568E-02 14.04058 at 10iterations 4.5141843E-03 0.6949902 at 20iterations 3.2417825E-04 6.1590195E-02 at 30iterations 3.7696434E-05 9.2248917E-03 at 40iterations 8.6375330E-06 2.4304390E-03 at 50iterations finished qdiffx linear iterations at : 17:09:00 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 8.6375330E-06 2.4304390E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.360000 DelPhi exited at 17:09:01 3.363u 0.175s 0:03.87 91.2% 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 Mon Oct 10 2011 at 17:09:01 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 = 2894 !!! WARNING: GLY 31 has a net charge of 0.5000 !!! WARNING: ALA 172 has a net charge of 0.5000 !!! WARNING: PRO 352 has a net charge of 0.5000 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: 1.631680 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): -34.40800 31.04600 ymin,ymax (A): -22.57000 25.10500 zmin,zma (A): -37.95900 6.852000 x,y,z range (A): 65.45400 47.67500 44.81100 scale (grids/A): 1.631680 object centre (A): -1.681001 1.267500 -15.55350 number of atom coordinates read : 2894 total number of charged atoms : 2754 net assigned charge : 0.5000146 assigned positive charge : 431.5321 centred at (gu) : 89.16010 91.03526 90.68888 assigned negative charge : -431.0332 centred at (gu) : 89.15684 90.56450 90.99303 start vw surface at 0.1100000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 60811 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26861 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 18563 mr = 39757 m= 1920 mr = 12754 m= 44 mr = 909 m= 0 mr = 2 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 89 time to turn everything in is 0.3200000 number of dielectric boundary points 27916 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 294 ## 6 charges are in solution ## iepsmp to db, and charging done at 0.4000000 number of grid points assigned charge 21052 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) : 0.5438934 object centre at (A) : -1.681001 1.267500 -15.55350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.3456299E-03 -3.0416267E-03 midg,1,midg; midg,igrid,midg -1.4668182E-02 1.0729642E-02 1,midg,midg; igrid,midg,midg 2.1916884E-03 -5.1419423E-03 gauss-seidel spectral radius is 0.9981744 estimated iterations to convergence 186 setup time was (sec) 0.5300000 now iterating at: 17:09:01 rms-change max change #iterations 3.259033 180.7344 at 10iterations 1.347876 63.42459 at 20iterations 0.5622482 22.38923 at 30iterations 0.2340225 9.126186 at 40iterations 9.6955158E-02 3.567090 at 50iterations 4.0349331E-02 1.471879 at 60iterations 1.6847741E-02 0.6382284 at 70iterations 7.0194788E-03 0.2626839 at 80iterations 2.9268852E-03 0.1006355 at 90iterations 1.2156332E-03 4.3460846E-02 at 100iterations 5.0906761E-04 1.8208265E-02 at 110iterations 2.1364850E-04 8.0187321E-03 at 120iterations finished qdiffx linear iterations at : 17:09:08 total time elapsed so far: 7.620000 # loops : 120 mean,max change (kT/e) : 2.1364850E-04 8.0187321E-03 energy calculations done at 7.620000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.760000 DelPhi exited at 17:09:09 7.761u 0.207s 0:08.80 90.4% 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 Mon Oct 10 2011 at 17:09:10 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 = 2894 !!! WARNING: GLY 31 has a net charge of 0.5000 !!! WARNING: ALA 172 has a net charge of 0.5000 !!! WARNING: PRO 352 has a net charge of 0.5000 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: 2.447520 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): -34.40800 31.04600 ymin,ymax (A): -22.57000 25.10500 zmin,zma (A): -37.95900 6.852000 x,y,z range (A): 65.45400 47.67500 44.81100 scale (grids/A): 2.447520 object centre (A): -1.681001 1.267500 -15.55350 number of atom coordinates read : 2894 total number of charged atoms : 2754 net assigned charge : 0.5000146 assigned positive charge : 431.5321 centred at (gu) : 88.74001 91.55254 91.03316 assigned negative charge : -431.0332 centred at (gu) : 88.73518 90.84658 91.48949 start vw surface at 0.1000000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 141242 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26861 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 63915 mr = 97985 m= 18343 mr = 50034 m= 2849 mr = 13776 m= 186 mr = 1884 m= 3 mr = 85 m= 0 mr = 0 time to grow re-entrant surface = 0.4000000 no. cavity mid-points inaccessible to solvent = 274 time to turn everything in is 0.7400000 number of dielectric boundary points 62774 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 18 iepsmp to db, and charging done at 0.8300000 number of grid points assigned charge 22013 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) : 1.631680 object centre at (A) : -1.681001 1.267500 -15.55350 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.0208170E-02 -3.8305659E-02 midg,1,midg; midg,igrid,midg -0.2141578 0.1765175 1,midg,midg; igrid,midg,midg 6.9758959E-02 8.5067533E-02 gauss-seidel spectral radius is 0.9991367 estimated iterations to convergence 269 setup time was (sec) 0.9700000 now iterating at: 17:09:11 rms-change max change #iterations 8.494449 301.1697 at 10iterations 4.751386 143.7267 at 20iterations 2.647014 63.18025 at 30iterations 1.469501 36.93312 at 40iterations 0.8103982 19.75514 at 50iterations 0.4473109 10.46220 at 60iterations 0.2463240 5.225685 at 70iterations 0.1357841 3.041218 at 80iterations 7.4623801E-02 1.594899 at 90iterations 4.1011427E-02 0.8413982 at 100iterations 2.2502566E-02 0.4618673 at 110iterations 1.2352222E-02 0.2762222 at 120iterations 6.7943376E-03 0.1452751 at 130iterations 3.7276498E-03 7.9482079E-02 at 140iterations 2.0429164E-03 4.3772697E-02 at 150iterations 1.1232485E-03 2.5850296E-02 at 160iterations 6.1443250E-04 1.2132823E-02 at 170iterations 3.3764658E-04 6.8478584E-03 at 180iterations finished qdiffx linear iterations at : 17:09:22 total time elapsed so far: 11.80000 # loops : 180 mean,max change (kT/e) : 3.3764658E-04 6.8478584E-03 energy calculations done at 11.80000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.93000 DelPhi exited at 17:09:22 11.931u 0.186s 0:12.78 94.7% 0+0k 0+0io 0pf+0w