Sun Oct 9 13:58:37 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 Sun Oct 9 2011 at 13:58:37 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2397 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.6967960 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): -5.788000 44.23000 ymin,ymax (A): 22.48700 73.57800 zmin,zma (A): 41.73100 84.46500 x,y,z range (A): 50.01800 51.09100 42.73400 scale (grids/A): 0.6967960 object centre (A): 19.22100 48.03250 63.09800 number of atom coordinates read : 2397 total number of charged atoms : 2256 net assigned charge : 4.500021 assigned positive charge : 365.8361 centred at (gu) : 89.49276 91.15406 90.62176 assigned negative charge : -361.3366 centred at (gu) : 89.48919 91.32912 90.67886 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 7858 nv = 96 ne = 84 npr = 48061 no. pairs analyzed = 48061 no. exposed pairs = 2938 no. arc points = 20670 no. surface atoms = 993 nbur = 1404 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 514 mr = 4374 m= 4 mr = 103 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3200000 number of dielectric boundary points 3899 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1966 ## 188 charges are in solution ## iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 8858 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.9715393E-08 5.2709814E-09 midg,1,midg; midg,igrid,midg 8.5876060E-08 -6.3001544E-08 1,midg,midg; igrid,midg,midg 3.2000347E-08 2.9273792E-08 gauss-seidel spectral radius is 0.9893011 estimated iterations to convergence 79 setup time was (sec) 0.5400000 now iterating at: 13:58:37 rms-change max change #iterations 0.2005883 30.71029 at 10iterations 2.4799770E-02 4.570850 at 20iterations 3.3834209E-03 0.4244347 at 30iterations 7.0404197E-04 0.1002121 at 40iterations 2.2372574E-04 3.4484863E-02 at 50iterations finished qdiffx linear iterations at : 13:58:40 total time elapsed so far: 2.950000 # loops : 50 mean,max change (kT/e) : 2.2372574E-04 3.4484863E-02 energy calculations done at 2.950000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.120000 DelPhi exited at 13:58:40 3.125u 0.147s 0:03.57 91.3% 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 Sun Oct 9 2011 at 13:58:40 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2397 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: 2.090388 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): -5.788000 44.23000 ymin,ymax (A): 22.48700 73.57800 zmin,zma (A): 41.73100 84.46500 x,y,z range (A): 50.01800 51.09100 42.73400 scale (grids/A): 2.090388 object centre (A): 19.22100 48.03250 63.09800 number of atom coordinates read : 2397 total number of charged atoms : 2256 net assigned charge : 4.500021 assigned positive charge : 365.8361 centred at (gu) : 88.47791 93.46180 91.86485 assigned negative charge : -361.3366 centred at (gu) : 88.46743 93.98713 92.03630 start vw surface at 0.1500000 fill in re-entrant regions at 0.2700000 boundary points on vw surface= 83395 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20670 grid for indexing accessible points = 1.400000 m= 32260 mr = 58149 m= 6012 mr = 24095 m= 562 mr = 3982 m= 9 mr = 302 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 113 time to turn everything in is 0.5900000 number of dielectric boundary points 35710 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 110 iepsmp to db, and charging done at 0.7000000 number of grid points assigned charge 17894 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) : 0.6967960 object centre at (A) : 19.22100 48.03250 63.09800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.6743618E-02 1.2670235E-02 midg,1,midg; midg,igrid,midg 1.5774261E-02 -5.0785284E-02 1,midg,midg; igrid,midg,midg 6.9918878E-02 1.0731978E-02 gauss-seidel spectral radius is 0.9988384 estimated iterations to convergence 232 setup time was (sec) 0.8500000 now iterating at: 13:58:41 rms-change max change #iterations 4.953076 234.8558 at 10iterations 2.446272 91.27211 at 20iterations 1.215757 34.69403 at 30iterations 0.6022822 18.80502 at 40iterations 0.3001774 8.687223 at 50iterations 0.1498105 4.116405 at 60iterations 7.4315794E-02 2.178398 at 70iterations 3.7050426E-02 1.066124 at 80iterations 1.8596884E-02 0.5221653 at 90iterations 9.4144447E-03 0.2952995 at 100iterations 4.8036044E-03 0.1349757 at 110iterations 2.5396487E-03 8.1573486E-02 at 120iterations finished qdiffx linear iterations at : 13:58:47 total time elapsed so far: 6.820000 # loops : 120 mean,max change (kT/e) : 2.5396487E-03 8.1573486E-02 energy calculations done at 6.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.990000 DelPhi exited at 13:58:48 6.994u 0.152s 0:07.43 96.0% 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 Sun Oct 9 2011 at 13:58:48 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2397 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.135582 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): -5.788000 44.23000 ymin,ymax (A): 22.48700 73.57800 zmin,zma (A): 41.73100 84.46500 x,y,z range (A): 50.01800 51.09100 42.73400 scale (grids/A): 3.135582 object centre (A): 19.22100 48.03250 63.09800 number of atom coordinates read : 2397 total number of charged atoms : 2256 net assigned charge : 4.500021 assigned positive charge : 365.8361 centred at (gu) : 87.71668 95.19258 92.79724 assigned negative charge : -361.3366 centred at (gu) : 87.70116 95.98058 93.05427 start vw surface at 0.1500000 fill in re-entrant regions at 0.8400000 boundary points on vw surface= 192103 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20670 grid for indexing accessible points = 1.400000 m= 101625 mr = 140351 m= 40104 mr = 83642 m= 11271 mr = 32667 m= 2368 mr = 8675 m= 280 mr = 1821 m= 3 mr = 185 m= 0 mr = 0 time to grow re-entrant surface = 0.8899999 no. cavity mid-points inaccessible to solvent = 336 time to turn everything in is 1.830000 number of dielectric boundary points 80413 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.950000 number of grid points assigned charge 18048 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) : 2.090388 object centre at (A) : 19.22100 48.03250 63.09800 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5586535 1.8436607E-02 midg,1,midg; midg,igrid,midg 0.3738800 -0.5491062 1,midg,midg; igrid,midg,midg 0.7828125 -0.1165363 gauss-seidel spectral radius is 0.9993019 estimated iterations to convergence 299 setup time was (sec) 2.100000 now iterating at: 13:58:50 rms-change max change #iterations 11.04657 368.1113 at 10iterations 6.564581 134.0757 at 20iterations 3.880000 84.09985 at 30iterations 2.294206 44.34280 at 40iterations 1.359250 25.79766 at 50iterations 0.7968907 13.18521 at 60iterations 0.4691227 8.225723 at 70iterations 0.2760362 4.497781 at 80iterations 0.1623993 2.942972 at 90iterations 9.5377736E-02 1.725478 at 100iterations 5.5970918E-02 0.8828468 at 110iterations 3.3003133E-02 0.5798998 at 120iterations 1.9609829E-02 0.3245087 at 130iterations 1.1780485E-02 0.2122498 at 140iterations 7.2497418E-03 0.1375465 at 150iterations 4.6531968E-03 9.4299316E-02 at 160iterations 3.1462382E-03 6.9646835E-02 at 170iterations 2.2818272E-03 5.2177429E-02 at 180iterations finished qdiffx linear iterations at : 13:58:59 total time elapsed so far: 11.55000 # loops : 180 mean,max change (kT/e) : 2.2818272E-03 5.2177429E-02 energy calculations done at 11.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.72000 DelPhi exited at 13:59:00 11.724u 0.187s 0:12.19 97.6% 0+0k 0+0io 0pf+0w