Sun Oct 9 16:09:38 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+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 Sun Oct 9 2011 at 16:09:38 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3066 !!! WARNING: GLM 162 has a net charge of -0.0940 !!! WARNING: GLM 231 has a net charge of -0.0940 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: 0.6319901 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): -15.42800 37.00900 ymin,ymax (A): 3.618000 56.30700 zmin,zma (A): -34.82500 21.50500 x,y,z range (A): 52.43700 52.68900 56.32999 scale (grids/A): 0.6319901 object centre (A): 10.79050 29.96250 -6.659999 number of atom coordinates read : 3066 total number of charged atoms : 2914 net assigned charge : -6.687979 assigned positive charge : 451.4991 centred at (gu) : 90.38676 91.19576 88.76165 assigned negative charge : -458.1885 centred at (gu) : 90.39128 91.33286 88.69380 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 8201 nv = 96 ne = 84 npr = 63105 no. pairs analyzed = 63105 no. exposed pairs = 3747 no. arc points = 26422 no. surface atoms = 1276 nbur = 1790 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 486 mr = 4546 m= 3 mr = 76 m= 0 mr = 0 time to grow re-entrant surface = 0.1300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 4068 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2559 ## 221 charges are in solution ## iepsmp to db, and charging done at 0.2900000 number of grid points assigned charge 9963 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.9462092E-08 -5.4594031E-11 midg,1,midg; midg,igrid,midg 5.6809091E-09 -2.9453494E-08 1,midg,midg; igrid,midg,midg -6.3419154E-09 -8.5306491E-09 gauss-seidel spectral radius is 0.9870718 estimated iterations to convergence 72 setup time was (sec) 0.4100000 now iterating at: 16:09:38 rms-change max change #iterations 0.1517139 18.99181 at 10iterations 1.4700660E-02 1.949209 at 20iterations 1.4381065E-03 0.1996307 at 30iterations 1.5641763E-04 2.1830559E-02 at 40iterations 2.6868111E-05 4.0695667E-03 at 50iterations finished qdiffx linear iterations at : 16:09:41 total time elapsed so far: 3.250000 # loops : 50 mean,max change (kT/e) : 2.6868111E-05 4.0695667E-03 energy calculations done at 3.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 16:09:42 3.384u 0.175s 0:03.99 88.9% 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 Sun Oct 9 2011 at 16:09:42 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3066 !!! WARNING: GLM 162 has a net charge of -0.0940 !!! WARNING: GLM 231 has a net charge of -0.0940 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: 1.895970 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): -15.42800 37.00900 ymin,ymax (A): 3.618000 56.30700 zmin,zma (A): -34.82500 21.50500 x,y,z range (A): 52.43700 52.68900 56.32999 scale (grids/A): 1.895970 object centre (A): 10.79050 29.96250 -6.659999 number of atom coordinates read : 3066 total number of charged atoms : 2914 net assigned charge : -6.687979 assigned positive charge : 451.4991 centred at (gu) : 91.15952 93.58652 86.28429 assigned negative charge : -458.1885 centred at (gu) : 91.17378 93.99805 86.08098 start vw surface at 0.1000000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 88909 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26422 grid for indexing accessible points = 1.400000 m= 32352 mr = 62321 m= 5703 mr = 23558 m= 365 mr = 3558 m= 2 mr = 124 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 37770 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 168 iepsmp to db, and charging done at 0.5100000 number of grid points assigned charge 22922 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) : 0.6319901 object centre at (A) : 10.79050 29.96250 -6.659999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1187908E-02 1.7398870E-02 midg,1,midg; midg,igrid,midg -1.9885551E-02 -4.1150782E-02 1,midg,midg; igrid,midg,midg -3.2076780E-02 -3.0266123E-02 gauss-seidel spectral radius is 0.9986660 estimated iterations to convergence 217 setup time was (sec) 0.6500000 now iterating at: 16:09:42 rms-change max change #iterations 4.622387 191.2742 at 10iterations 2.179296 75.46639 at 20iterations 1.034066 31.08328 at 30iterations 0.4864167 15.07360 at 40iterations 0.2294644 6.875801 at 50iterations 0.1085713 3.161805 at 60iterations 5.1424939E-02 1.613060 at 70iterations 2.4282506E-02 0.6654053 at 80iterations 1.1476198E-02 0.3481637 at 90iterations 5.4550762E-03 0.1536522 at 100iterations 2.6001777E-03 7.9114914E-02 at 110iterations 1.2564005E-03 3.8959503E-02 at 120iterations finished qdiffx linear iterations at : 16:09:50 total time elapsed so far: 7.760000 # loops : 120 mean,max change (kT/e) : 1.2564005E-03 3.8959503E-02 energy calculations done at 7.760000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.890000 DelPhi exited at 16:09:50 7.893u 0.189s 0:08.39 96.1% 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 Sun Oct 9 2011 at 16:09:50 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: 270 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3066 !!! WARNING: GLM 162 has a net charge of -0.0940 !!! WARNING: GLM 231 has a net charge of -0.0940 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: 2.843956 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): -15.42800 37.00900 ymin,ymax (A): 3.618000 56.30700 zmin,zma (A): -34.82500 21.50500 x,y,z range (A): 52.43700 52.68900 56.32999 scale (grids/A): 2.843956 object centre (A): 10.79050 29.96250 -6.659999 number of atom coordinates read : 3066 total number of charged atoms : 2914 net assigned charge : -6.687979 assigned positive charge : 451.4991 centred at (gu) : 91.73893 95.37943 84.42613 assigned negative charge : -458.1885 centred at (gu) : 91.76059 95.99709 84.12132 start vw surface at 0.1000000 fill in re-entrant regions at 0.3700000 boundary points on vw surface= 206007 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26422 grid for indexing accessible points = 1.400000 m= 103713 mr = 151385 m= 38991 mr = 84409 m= 10326 mr = 30877 m= 1543 mr = 7778 m= 100 mr = 1001 m= 1 mr = 42 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.120000 number of dielectric boundary points 85189 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.210000 number of grid points assigned charge 23310 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) : 1.895970 object centre at (A) : 10.79050 29.96250 -6.659999 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.8170278E-02 0.3558036 midg,1,midg; midg,igrid,midg -0.3493795 -0.4092526 1,midg,midg; igrid,midg,midg -0.4181986 -0.3279688 gauss-seidel spectral radius is 0.9992798 estimated iterations to convergence 294 setup time was (sec) 1.360000 now iterating at: 16:09:52 rms-change max change #iterations 10.90167 504.0015 at 10iterations 6.458599 138.7542 at 20iterations 3.803283 76.29802 at 30iterations 2.228356 42.29683 at 40iterations 1.307733 24.21283 at 50iterations 0.7638022 15.06385 at 60iterations 0.4460098 8.537033 at 70iterations 0.2597100 4.624516 at 80iterations 0.1511745 3.207338 at 90iterations 8.7719500E-02 1.626587 at 100iterations 5.0935712E-02 0.8531246 at 110iterations 2.9649597E-02 0.5919724 at 120iterations 1.7207948E-02 0.3074398 at 130iterations 9.9984361E-03 0.1697750 at 140iterations 5.7965219E-03 0.1015396 at 150iterations 3.3660030E-03 6.4702988E-02 at 160iterations 1.9533180E-03 3.4544468E-02 at 170iterations 1.1400734E-03 2.0618439E-02 at 180iterations finished qdiffx linear iterations at : 16:10:03 total time elapsed so far: 12.74000 # loops : 180 mean,max change (kT/e) : 1.1400734E-03 2.0618439E-02 energy calculations done at 12.74000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.88000 DelPhi exited at 16:10:03 12.880u 0.198s 0:13.34 97.9% 0+0k 0+0io 0pf+0w