Sat Oct 8 21:06:38 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 Sat Oct 8 2011 at 21:06:38 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2584 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 636 has a net charge of 1.4000 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: 0.6200578 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): -31.44300 17.26700 ymin,ymax (A): -23.58900 22.60500 zmin,zma (A): -12.49200 44.92200 x,y,z range (A): 48.71000 46.19400 57.41400 scale (grids/A): 0.6200578 object centre (A): -7.088000 -0.4919996 16.21500 number of atom coordinates read : 2584 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 88.53152 89.22024 89.59424 assigned negative charge : -388.8955 centred at (gu) : 88.40919 89.27777 89.47906 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6428 nv = 96 ne = 84 npr = 53602 no. pairs analyzed = 53602 no. exposed pairs = 3055 no. arc points = 21793 no. surface atoms = 1012 nbur = 1572 mkacc time = 9.0000004E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 294 mr = 3521 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 9.9999994E-02 no. cavity mid-points inaccessible to solvent = 98 time to turn everything in is 0.2100000 number of dielectric boundary points 3179 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2230 ## 248 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8128 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.3944652E-09 1.0358328E-08 midg,1,midg; midg,igrid,midg 8.9821430E-09 -4.3253581E-11 1,midg,midg; igrid,midg,midg -6.3433170E-09 8.5494101E-09 gauss-seidel spectral radius is 0.9865255 estimated iterations to convergence 71 setup time was (sec) 0.4100000 now iterating at: 21:06:39 rms-change max change #iterations 0.1299324 22.50996 at 10iterations 1.1563607E-02 1.942673 at 20iterations 1.0791310E-03 0.1913948 at 30iterations 9.9864636E-05 1.5167236E-02 at 40iterations 9.1578195E-06 1.3389587E-03 at 50iterations finished qdiffx linear iterations at : 21:06:42 total time elapsed so far: 3.390000 # loops : 50 mean,max change (kT/e) : 9.1578195E-06 1.3389587E-03 energy calculations done at 3.390000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.530000 DelPhi exited at 21:06:42 3.529u 0.172s 0:03.97 92.9% 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 Sat Oct 8 2011 at 21:06:42 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2584 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 636 has a net charge of 1.4000 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: 1.860173 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): -31.44300 17.26700 ymin,ymax (A): -23.58900 22.60500 zmin,zma (A): -12.49200 44.92200 x,y,z range (A): 48.71000 46.19400 57.41400 scale (grids/A): 1.860173 object centre (A): -7.088000 -0.4919996 16.21500 number of atom coordinates read : 2584 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 85.59386 87.66006 88.78228 assigned negative charge : -388.8955 centred at (gu) : 85.22749 87.83311 88.43696 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 70472 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21793 grid for indexing accessible points = 1.400000 m= 23701 mr = 49042 m= 3106 mr = 17186 m= 136 mr = 1763 m= 2 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 4655 time to turn everything in is 0.3500000 number of dielectric boundary points 29404 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 159 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 19347 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) : 0.6200578 object centre at (A) : -7.088000 -0.4919996 16.21500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3467040E-02 1.9806096E-02 midg,1,midg; midg,igrid,midg 1.3162966E-02 1.8123777E-03 1,midg,midg; igrid,midg,midg -3.5514270E-03 4.1146070E-02 gauss-seidel spectral radius is 0.9985662 estimated iterations to convergence 209 setup time was (sec) 0.5800000 now iterating at: 21:06:43 rms-change max change #iterations 4.032872 169.3801 at 10iterations 1.848484 61.56499 at 20iterations 0.8465370 30.78645 at 30iterations 0.3902856 12.62982 at 40iterations 0.1791077 6.494874 at 50iterations 8.2385316E-02 2.843982 at 60iterations 3.7978962E-02 1.436141 at 70iterations 1.7447131E-02 0.5690575 at 80iterations 8.0007054E-03 0.2623291 at 90iterations 3.6870432E-03 0.1331501 at 100iterations 1.6949960E-03 5.3852081E-02 at 110iterations 7.7955000E-04 2.6026726E-02 at 120iterations finished qdiffx linear iterations at : 21:06:50 total time elapsed so far: 7.900000 # loops : 120 mean,max change (kT/e) : 7.7955000E-04 2.6026726E-02 energy calculations done at 7.900000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.040000 DelPhi exited at 21:06:51 8.041u 0.199s 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 Sat Oct 8 2011 at 21:06:51 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2584 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 636 has a net charge of 1.4000 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: 2.790260 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): -31.44300 17.26700 ymin,ymax (A): -23.58900 22.60500 zmin,zma (A): -12.49200 44.92200 x,y,z range (A): 48.71000 46.19400 57.41400 scale (grids/A): 2.790260 object centre (A): -7.088000 -0.4919996 16.21500 number of atom coordinates read : 2584 total number of charged atoms : 2466 net assigned charge : 4.500007 assigned positive charge : 393.3950 centred at (gu) : 83.39071 86.49005 88.17338 assigned negative charge : -388.8955 centred at (gu) : 82.84117 86.74969 87.65533 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 163343 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21793 grid for indexing accessible points = 1.400000 m= 79278 mr = 118934 m= 25779 mr = 64737 m= 5277 mr = 20302 m= 565 mr = 3683 m= 21 mr = 330 m= 1 mr = 3 m= 0 mr = 0 time to grow re-entrant surface = 0.4700000 no. cavity mid-points inaccessible to solvent = 15539 time to turn everything in is 0.8600000 number of dielectric boundary points 66275 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 0.9500000 number of grid points assigned charge 19723 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) : 1.860173 object centre at (A) : -7.088000 -0.4919996 16.21500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.2363101 0.2274585 midg,1,midg; midg,igrid,midg 0.1508456 9.7716963E-03 1,midg,midg; igrid,midg,midg -3.9968226E-02 0.5453388 gauss-seidel spectral radius is 0.9992349 estimated iterations to convergence 285 setup time was (sec) 1.100000 now iterating at: 21:06:52 rms-change max change #iterations 9.486616 336.7101 at 10iterations 5.428337 130.1324 at 20iterations 3.096305 63.23681 at 30iterations 1.766041 33.68793 at 40iterations 1.005109 24.32462 at 50iterations 0.5716105 11.54993 at 60iterations 0.3260761 6.266657 at 70iterations 0.1850661 3.524268 at 80iterations 0.1054431 1.901768 at 90iterations 5.9904374E-02 1.109127 at 100iterations 3.4026518E-02 0.6357079 at 110iterations 1.9358266E-02 0.4040489 at 120iterations 1.1006107E-02 0.2112446 at 130iterations 6.2451009E-03 0.1192303 at 140iterations 3.5492904E-03 6.4928055E-02 at 150iterations 2.0245288E-03 3.9270401E-02 at 160iterations 1.1519667E-03 2.0547867E-02 at 170iterations 6.5358152E-04 1.2330055E-02 at 180iterations finished qdiffx linear iterations at : 21:07:04 total time elapsed so far: 12.69000 # loops : 180 mean,max change (kT/e) : 6.5358152E-04 1.2330055E-02 energy calculations done at 12.69000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.81000 DelPhi exited at 21:07:04 12.816u 0.225s 0:13.39 97.3% 0+0k 0+0io 0pf+0w