Sat Oct 8 11:38:08 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 11:38:09 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3093 !!! WARNING: HIR 281 has a net charge of 0.5140 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: 0.5621437 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): 6.100000 67.26000 ymin,ymax (A): -8.080000 38.94700 zmin,zma (A): -24.95000 38.37900 x,y,z range (A): 61.16000 47.02700 63.32900 scale (grids/A): 0.5621437 object centre (A): 36.68000 15.43350 6.714501 number of atom coordinates read : 3093 total number of charged atoms : 2948 net assigned charge : -9.985970 assigned positive charge : 460.4777 centred at (gu) : 88.26002 90.39906 91.75800 assigned negative charge : -470.4646 centred at (gu) : 88.18015 90.46206 91.84954 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6329 nv = 96 ne = 84 npr = 63188 no. pairs analyzed = 63188 no. exposed pairs = 3964 no. arc points = 27275 no. surface atoms = 1350 nbur = 1743 mkacc time = 9.9999994E-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 = 1.540000 m= 316 mr = 3316 m= 1 mr = 31 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3299 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2691 ## 304 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 8279 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.1691923E-11 -3.4516225E-09 midg,1,midg; midg,igrid,midg -2.8631403E-10 -2.0798248E-09 1,midg,midg; igrid,midg,midg -3.2061289E-09 -8.2132377E-11 gauss-seidel spectral radius is 0.9836838 estimated iterations to convergence 64 setup time was (sec) 0.4600000 now iterating at: 11:38:09 rms-change max change #iterations 8.7361902E-02 17.87053 at 10iterations 7.5570568E-03 1.189728 at 20iterations 2.2837459E-03 0.4265575 at 30iterations 1.1201311E-03 0.2109680 at 40iterations 5.6061544E-04 0.1048889 at 50iterations finished qdiffx linear iterations at : 11:38:13 total time elapsed so far: 3.770000 # loops : 50 mean,max change (kT/e) : 5.6061544E-04 0.1048889 energy calculations done at 3.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.890000 DelPhi exited at 11:38:13 3.894u 0.237s 0:04.71 87.4% 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 Sat Oct 8 2011 at 11:38:13 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3093 !!! WARNING: HIR 281 has a net charge of 0.5140 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: 1.686431 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): 6.100000 67.26000 ymin,ymax (A): -8.080000 38.94700 zmin,zma (A): -24.95000 38.37900 x,y,z range (A): 61.16000 47.02700 63.32900 scale (grids/A): 1.686431 object centre (A): 36.68000 15.43350 6.714501 number of atom coordinates read : 3093 total number of charged atoms : 2948 net assigned charge : -9.985970 assigned positive charge : 460.4777 centred at (gu) : 84.77891 91.19601 95.27268 assigned negative charge : -470.4646 centred at (gu) : 84.53972 91.38550 95.54836 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 70632 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27275 grid for indexing accessible points = 1.400000 m= 22899 mr = 48447 m= 2826 mr = 15929 m= 97 mr = 1510 m= 2 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3700000 number of dielectric boundary points 30560 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 228 iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 22754 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) : 0.5621437 object centre at (A) : 36.68000 15.43350 6.714501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.3438108E-03 -2.8215166E-02 midg,1,midg; midg,igrid,midg -8.5246060E-03 -1.2968647E-02 1,midg,midg; igrid,midg,midg -1.4526061E-02 -5.1635629E-03 gauss-seidel spectral radius is 0.9983067 estimated iterations to convergence 193 setup time was (sec) 0.6300000 now iterating at: 11:38:14 rms-change max change #iterations 3.657342 182.9560 at 10iterations 1.569030 58.64224 at 20iterations 0.6770990 23.73286 at 30iterations 0.2913334 10.07028 at 40iterations 0.1257305 4.300552 at 50iterations 5.4446552E-02 1.970997 at 60iterations 2.3926558E-02 0.8579350 at 70iterations 1.0902486E-02 0.3858376 at 80iterations 5.5218264E-03 0.2107964 at 90iterations 3.2930863E-03 0.1265678 at 100iterations 2.2939446E-03 8.5582733E-02 at 110iterations 1.7312588E-03 6.5549850E-02 at 120iterations finished qdiffx linear iterations at : 11:38:23 total time elapsed so far: 8.800000 # loops : 120 mean,max change (kT/e) : 1.7312588E-03 6.5549850E-02 energy calculations done at 8.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.920000 DelPhi exited at 11:38:23 8.927u 0.355s 0:09.71 95.4% 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 Sat Oct 8 2011 at 11:38:23 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: 310 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3093 !!! WARNING: HIR 281 has a net charge of 0.5140 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: 2.529647 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): 6.100000 67.26000 ymin,ymax (A): -8.080000 38.94700 zmin,zma (A): -24.95000 38.37900 x,y,z range (A): 61.16000 47.02700 63.32900 scale (grids/A): 2.529647 object centre (A): 36.68000 15.43350 6.714501 number of atom coordinates read : 3093 total number of charged atoms : 2948 net assigned charge : -9.985970 assigned positive charge : 460.4777 centred at (gu) : 82.16817 91.79392 97.90878 assigned negative charge : -470.4646 centred at (gu) : 81.80948 92.07817 98.32236 start vw surface at 0.1000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 164096 reading accessible surface arcs data from file ARCDAT no. of arc points read = 27275 grid for indexing accessible points = 1.400000 m= 77773 mr = 118639 m= 23739 mr = 61648 m= 4673 mr = 17975 m= 427 mr = 3224 m= 6 mr = 178 m= 0 mr = 1 time to grow re-entrant surface = 0.5200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.9400000 number of dielectric boundary points 69049 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 14 iepsmp to db, and charging done at 1.060000 number of grid points assigned charge 23564 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) : 1.686431 object centre at (A) : 36.68000 15.43350 6.714501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.3541328E-02 -0.2435424 midg,1,midg; midg,igrid,midg -0.1629566 -0.1556051 1,midg,midg; igrid,midg,midg -0.3540985 -5.6917503E-02 gauss-seidel spectral radius is 0.9991765 estimated iterations to convergence 275 setup time was (sec) 1.240000 now iterating at: 11:38:25 rms-change max change #iterations 9.388497 277.6280 at 10iterations 5.366573 133.1447 at 20iterations 3.060211 73.15470 at 30iterations 1.730434 39.82307 at 40iterations 0.9768064 20.85973 at 50iterations 0.5504421 10.57593 at 60iterations 0.3091559 6.366777 at 70iterations 0.1737021 3.483805 at 80iterations 9.7171322E-02 2.066139 at 90iterations 5.4459184E-02 1.048807 at 100iterations 3.0599723E-02 0.6390686 at 110iterations 1.7161246E-02 0.3488851 at 120iterations 9.7240964E-03 0.2100487 at 130iterations 5.5806008E-03 0.1136799 at 140iterations 3.3378897E-03 6.8256378E-02 at 150iterations 2.1181286E-03 5.4924011E-02 at 160iterations 1.4681101E-03 3.2207489E-02 at 170iterations 1.1115753E-03 2.6594162E-02 at 180iterations finished qdiffx linear iterations at : 11:38:38 total time elapsed so far: 14.93000 # loops : 180 mean,max change (kT/e) : 1.1115753E-03 2.6594162E-02 energy calculations done at 14.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.06000 DelPhi exited at 11:38:39 15.066u 0.319s 0:15.72 97.7% 0+0k 0+0io 0pf+0w