Sat Oct 8 17:44:55 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+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 Sat Oct 8 2011 at 17:44:55 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3511 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5191926 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): -0.1000000 44.49100 ymin,ymax (A): -30.76900 26.07900 zmin,zma (A): 0.8839999 69.45200 x,y,z range (A): 44.59100 56.84800 68.56800 scale (grids/A): 0.5191926 object centre (A): 22.19550 -2.345000 35.16800 number of atom coordinates read : 3511 total number of charged atoms : 3364 net assigned charge : -5.871982 assigned positive charge : 538.3141 centred at (gu) : 90.28704 91.81145 90.69556 assigned negative charge : -544.1879 centred at (gu) : 90.24097 91.76532 90.68994 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 5996 nv = 96 ne = 84 npr = 71559 no. pairs analyzed = 71559 no. exposed pairs = 4252 no. arc points = 29088 no. surface atoms = 1455 nbur = 2056 mkacc time = 0.1500000 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 = 1.652000 m= 224 mr = 3182 m= 0 mr = 6 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3032 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2961 ## 434 charges are in solution ## iepsmp to db, and charging done at 0.4500000 number of grid points assigned charge 8005 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.1749171E-10 -1.2897207E-10 midg,1,midg; midg,igrid,midg -1.6074510E-10 1.2926982E-11 1,midg,midg; igrid,midg,midg -2.3690874E-10 6.0670019E-12 gauss-seidel spectral radius is 0.9809289 estimated iterations to convergence 60 setup time was (sec) 0.5700000 now iterating at: 17:44:56 rms-change max change #iterations 6.2781759E-02 10.65563 at 10iterations 3.8178593E-03 0.6216240 at 20iterations 3.5107826E-04 6.0612679E-02 at 30iterations 6.7991539E-05 1.2698174E-02 at 40iterations 1.6732864E-05 2.9048920E-03 at 50iterations finished qdiffx linear iterations at : 17:44:59 total time elapsed so far: 3.260000 # loops : 50 mean,max change (kT/e) : 1.6732864E-05 2.9048920E-03 energy calculations done at 3.260000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.440000 DelPhi exited at 17:44:59 3.444u 0.195s 0:03.93 92.3% 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 17:44:59 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3511 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.557578 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): -0.1000000 44.49100 ymin,ymax (A): -30.76900 26.07900 zmin,zma (A): 0.8839999 69.45200 x,y,z range (A): 44.59100 56.84800 68.56800 scale (grids/A): 1.557578 object centre (A): 22.19550 -2.345000 35.16800 number of atom coordinates read : 3511 total number of charged atoms : 3364 net assigned charge : -5.871982 assigned positive charge : 538.3141 centred at (gu) : 90.86024 95.43332 92.08602 assigned negative charge : -544.1879 centred at (gu) : 90.72232 95.29549 92.06944 start vw surface at 0.1500000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 67942 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29088 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 20418 mr = 47379 m= 1775 mr = 13925 m= 40 mr = 798 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 94 time to turn everything in is 0.4900000 number of dielectric boundary points 28073 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 423 ## 5 charges are in solution ## iepsmp to db, and charging done at 0.6000000 number of grid points assigned charge 25426 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) : 0.5191926 object centre at (A) : 22.19550 -2.345000 35.16800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3522109E-03 1.1505340E-02 midg,1,midg; midg,igrid,midg -7.7862404E-03 -1.0474048E-02 1,midg,midg; igrid,midg,midg -4.1944273E-03 1.8186283E-03 gauss-seidel spectral radius is 0.9980378 estimated iterations to convergence 179 setup time was (sec) 0.7700000 now iterating at: 17:45:00 rms-change max change #iterations 3.335455 144.0995 at 10iterations 1.341291 47.44839 at 20iterations 0.5399801 18.42570 at 30iterations 0.2182756 8.129356 at 40iterations 8.8023983E-02 3.592191 at 50iterations 3.5563536E-02 1.356850 at 60iterations 1.4386340E-02 0.4855206 at 70iterations 5.8288621E-03 0.2205944 at 80iterations 2.3791147E-03 9.0866089E-02 at 90iterations 9.8156824E-04 3.6294937E-02 at 100iterations 4.2243898E-04 1.6703606E-02 at 110iterations 1.9067802E-04 8.0938339E-03 at 120iterations finished qdiffx linear iterations at : 17:45:07 total time elapsed so far: 7.600000 # loops : 120 mean,max change (kT/e) : 1.9067802E-04 8.0938339E-03 energy calculations done at 7.600000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.790000 DelPhi exited at 17:45:08 7.788u 0.260s 0:08.31 96.7% 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 17:45:08 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: 325 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3511 !!! WARNING: ASL 294 has a net charge of -0.1000 !!! WARNING: ILE 447 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 2.336367 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): -0.1000000 44.49100 ymin,ymax (A): -30.76900 26.07900 zmin,zma (A): 0.8839999 69.45200 x,y,z range (A): 44.59100 56.84800 68.56800 scale (grids/A): 2.336367 object centre (A): 22.19550 -2.345000 35.16800 number of atom coordinates read : 3511 total number of charged atoms : 3364 net assigned charge : -5.871982 assigned positive charge : 538.3141 centred at (gu) : 91.29005 98.14949 93.12872 assigned negative charge : -544.1879 centred at (gu) : 91.08346 97.94324 93.10418 start vw surface at 0.1500000 fill in re-entrant regions at 0.3900000 boundary points on vw surface= 158072 reading accessible surface arcs data from file ARCDAT no. of arc points read = 29088 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.540000 m= 72725 mr = 115719 m= 18861 mr = 57825 m= 2605 mr = 13856 m= 142 mr = 1604 m= 4 mr = 60 m= 0 mr = 0 time to grow re-entrant surface = 0.6600000 no. cavity mid-points inaccessible to solvent = 364 time to turn everything in is 1.160000 number of dielectric boundary points 63345 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 49 iepsmp to db, and charging done at 1.300000 number of grid points assigned charge 26846 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) : 1.557578 object centre at (A) : 22.19550 -2.345000 35.16800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1504786 0.1119317 midg,1,midg; midg,igrid,midg -0.1097602 -0.1411116 1,midg,midg; igrid,midg,midg -7.6007247E-02 4.6317603E-02 gauss-seidel spectral radius is 0.9990950 estimated iterations to convergence 263 setup time was (sec) 1.470000 now iterating at: 17:45:09 rms-change max change #iterations 8.905668 344.6530 at 10iterations 4.926067 126.9553 at 20iterations 2.712893 70.88281 at 30iterations 1.482481 36.91951 at 40iterations 0.8096654 18.08165 at 50iterations 0.4402946 9.503834 at 60iterations 0.2398927 4.778687 at 70iterations 0.1303496 2.752622 at 80iterations 7.0778452E-02 1.411613 at 90iterations 3.8364906E-02 0.7623711 at 100iterations 2.0840680E-02 0.4338207 at 110iterations 1.1280131E-02 0.2389622 at 120iterations 6.1204350E-03 0.1278706 at 130iterations 3.3193752E-03 7.3251724E-02 at 140iterations 1.7993905E-03 3.6769867E-02 at 150iterations 9.7728928E-04 1.9665241E-02 at 160iterations 5.3357432E-04 1.2033463E-02 at 170iterations 2.9211212E-04 6.1191320E-03 at 180iterations finished qdiffx linear iterations at : 17:45:20 total time elapsed so far: 12.51000 # loops : 180 mean,max change (kT/e) : 2.9211212E-04 6.1191320E-03 energy calculations done at 12.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.69000 DelPhi exited at 17:45:21 12.694u 0.260s 0:13.22 97.9% 0+0k 0+0io 0pf+0w