Mon Oct 10 09:11:24 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 Mon Oct 10 2011 at 09:11:24 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6327651 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): -4.358000 35.51300 ymin,ymax (A): -4.119000 49.23300 zmin,zma (A): -24.59800 31.66300 x,y,z range (A): 39.87100 53.35200 56.26100 scale (grids/A): 0.6327651 object centre (A): 15.57750 22.55700 3.532500 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 292.9999 centred at (gu) : 90.18669 92.10499 89.99904 assigned negative charge : -290.0002 centred at (gu) : 90.28513 92.21466 89.94217 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5346 nv = 96 ne = 84 npr = 40418 no. pairs analyzed = 40418 no. exposed pairs = 2440 no. arc points = 17101 no. surface atoms = 826 nbur = 1144 mkacc time = 0.1300000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 263 mr = 2978 m= 1 mr = 28 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 37 time to turn everything in is 0.3300000 number of dielectric boundary points 2604 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1721 ## 164 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 6290 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.3294531E-10 7.7443607E-09 midg,1,midg; midg,igrid,midg 7.2833282E-09 -6.7929355E-09 1,midg,midg; igrid,midg,midg 1.0226984E-08 -3.4851724E-09 gauss-seidel spectral radius is 0.9870068 estimated iterations to convergence 72 setup time was (sec) 0.6100000 now iterating at: 09:11:25 rms-change max change #iterations 0.1216809 22.18608 at 10iterations 1.1367856E-02 2.013008 at 20iterations 1.1161898E-03 0.2020278 at 30iterations 1.0646047E-04 2.0169258E-02 at 40iterations 1.0044925E-05 1.7318726E-03 at 50iterations finished qdiffx linear iterations at : 09:11:29 total time elapsed so far: 4.420000 # loops : 50 mean,max change (kT/e) : 1.0044925E-05 1.7318726E-03 energy calculations done at 4.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.640000 DelPhi exited at 09:11:29 4.643u 0.436s 0:05.39 94.0% 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 09:11:29 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.898295 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): -4.358000 35.51300 ymin,ymax (A): -4.119000 49.23300 zmin,zma (A): -24.59800 31.66300 x,y,z range (A): 39.87100 53.35200 56.26100 scale (grids/A): 1.898295 object centre (A): 15.57750 22.55700 3.532500 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 292.9999 centred at (gu) : 90.55984 96.31493 89.99701 assigned negative charge : -290.0002 centred at (gu) : 90.85538 96.64425 89.82664 start vw surface at 0.1300000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 57579 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17101 grid for indexing accessible points = 1.400000 m= 21020 mr = 39789 m= 3008 mr = 16004 m= 161 mr = 1937 m= 3 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 2308 time to turn everything in is 0.6100000 number of dielectric boundary points 23980 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 131 iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 14458 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) : 0.6327651 object centre at (A) : 15.57750 22.55700 3.532500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6594830E-02 5.6127473E-03 midg,1,midg; midg,igrid,midg 3.3113953E-02 -1.0511060E-03 1,midg,midg; igrid,midg,midg 9.5869927E-03 -4.0134825E-03 gauss-seidel spectral radius is 0.9985489 estimated iterations to convergence 208 setup time was (sec) 0.9400000 now iterating at: 09:11:31 rms-change max change #iterations 3.596324 181.1368 at 10iterations 1.645470 64.73072 at 20iterations 0.7515998 30.82943 at 30iterations 0.3449728 11.25195 at 40iterations 0.1574270 5.959534 at 50iterations 7.1981154E-02 2.653588 at 60iterations 3.2928754E-02 1.135382 at 70iterations 1.5027195E-02 0.5465453 at 80iterations 6.8793055E-03 0.2434082 at 90iterations 3.1569032E-03 0.1143646 at 100iterations 1.4383210E-03 5.1663399E-02 at 110iterations 6.5719668E-04 2.4417877E-02 at 120iterations finished qdiffx linear iterations at : 09:11:40 total time elapsed so far: 10.43000 # loops : 120 mean,max change (kT/e) : 6.5719668E-04 2.4417877E-02 energy calculations done at 10.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.64000 DelPhi exited at 09:11:41 10.648u 0.493s 0:11.43 97.3% 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 Mon Oct 10 2011 at 09:11:41 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: 251 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1970 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.847443 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): -4.358000 35.51300 ymin,ymax (A): -4.119000 49.23300 zmin,zma (A): -24.59800 31.66300 x,y,z range (A): 39.87100 53.35200 56.26100 scale (grids/A): 2.847443 object centre (A): 15.57750 22.55700 3.532500 number of atom coordinates read : 1970 total number of charged atoms : 1838 net assigned charge : 3.000004 assigned positive charge : 292.9999 centred at (gu) : 90.83971 99.47236 89.99532 assigned negative charge : -290.0002 centred at (gu) : 91.28302 99.96643 89.73999 start vw surface at 0.1300000 fill in re-entrant regions at 0.5100000 boundary points on vw surface= 133105 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17101 grid for indexing accessible points = 1.400000 m= 67699 mr = 96017 m= 24347 mr = 56400 m= 5170 mr = 20178 m= 639 mr = 3916 m= 39 mr = 456 m= 0 mr = 14 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 7703 time to turn everything in is 1.550000 number of dielectric boundary points 54018 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.690000 number of grid points assigned charge 14703 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) : 1.898295 object centre at (A) : 15.57750 22.55700 3.532500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.060851 -3.6214810E-02 midg,1,midg; midg,igrid,midg 0.3514806 -7.5874761E-02 1,midg,midg; igrid,midg,midg 7.2722286E-02 -3.2576442E-02 gauss-seidel spectral radius is 0.9992197 estimated iterations to convergence 283 setup time was (sec) 1.910000 now iterating at: 09:11:43 rms-change max change #iterations 8.398958 323.1193 at 10iterations 4.790428 123.7454 at 20iterations 2.700387 58.11228 at 30iterations 1.529792 31.54463 at 40iterations 0.8614912 17.76313 at 50iterations 0.4882739 10.11770 at 60iterations 0.2745139 6.110398 at 70iterations 0.1551438 3.085701 at 80iterations 8.7674193E-02 1.927505 at 90iterations 4.9443115E-02 1.013779 at 100iterations 2.7925333E-02 0.6058164 at 110iterations 1.5702566E-02 0.3181229 at 120iterations 8.8656116E-03 0.1794758 at 130iterations 5.0127953E-03 9.5878601E-02 at 140iterations 2.8270634E-03 5.8738708E-02 at 150iterations 1.5978584E-03 3.3109665E-02 at 160iterations 9.0112531E-04 1.7647743E-02 at 170iterations 5.0893374E-04 1.0460377E-02 at 180iterations finished qdiffx linear iterations at : 09:11:59 total time elapsed so far: 17.48000 # loops : 180 mean,max change (kT/e) : 5.0893374E-04 1.0460377E-02 energy calculations done at 17.48000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 17.70000 DelPhi exited at 09:11:59 17.700u 0.501s 0:18.53 98.2% 0+0k 0+0io 0pf+0w