Sat Oct 8 22:35:38 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 Sat Oct 8 2011 at 22:35:38 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2316 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: 0.6304009 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): -27.07400 26.19700 ymin,ymax (A): 8.148999 50.58500 zmin,zma (A): -12.69300 43.77900 x,y,z range (A): 53.27100 42.43600 56.47200 scale (grids/A): 0.6304009 object centre (A): -0.4384995 29.36700 15.54300 number of atom coordinates read : 2316 total number of charged atoms : 2182 net assigned charge : 11.50003 assigned positive charge : 338.3774 centred at (gu) : 90.63805 91.37298 90.85384 assigned negative charge : -326.8781 centred at (gu) : 90.66771 91.32099 90.85592 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 6345 nv = 96 ne = 84 npr = 45883 no. pairs analyzed = 45883 no. exposed pairs = 3153 no. arc points = 22487 no. surface atoms = 1051 nbur = 1265 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 375 mr = 3266 m= 0 mr = 26 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3100000 number of dielectric boundary points 3428 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2218 ## 222 charges are in solution ## iepsmp to db, and charging done at 0.4100000 number of grid points assigned charge 7602 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.0656175E-08 1.4862702E-08 midg,1,midg; midg,igrid,midg 6.5493788E-09 2.2079863E-08 1,midg,midg; igrid,midg,midg 1.2938366E-08 1.1805487E-08 gauss-seidel spectral radius is 0.9869504 estimated iterations to convergence 72 setup time was (sec) 0.5200000 now iterating at: 22:35:38 rms-change max change #iterations 0.1232437 22.93198 at 10iterations 1.1699189E-02 1.765025 at 20iterations 1.1592440E-03 0.1906414 at 30iterations 1.4020634E-04 1.9164085E-02 at 40iterations 2.6920918E-05 3.6807060E-03 at 50iterations finished qdiffx linear iterations at : 22:35:41 total time elapsed so far: 2.990000 # loops : 50 mean,max change (kT/e) : 2.6920918E-05 3.6807060E-03 energy calculations done at 2.990000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.170000 DelPhi exited at 22:35:41 3.173u 0.165s 0:03.61 92.2% 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 22:35:41 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2316 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1300000 grid size : 179 scale,in grids/A, set to be: 1.891203 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): -27.07400 26.19700 ymin,ymax (A): 8.148999 50.58500 zmin,zma (A): -12.69300 43.77900 x,y,z range (A): 53.27100 42.43600 56.47200 scale (grids/A): 1.891203 object centre (A): -0.4384995 29.36700 15.54300 number of atom coordinates read : 2316 total number of charged atoms : 2182 net assigned charge : 11.50003 assigned positive charge : 338.3774 centred at (gu) : 91.91392 94.11848 92.56144 assigned negative charge : -326.8781 centred at (gu) : 92.00321 93.96298 92.56787 start vw surface at 0.2100000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 67920 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22487 grid for indexing accessible points = 1.400000 m= 24397 mr = 45214 m= 3930 mr = 17241 m= 234 mr = 2247 m= 5 mr = 79 m= 0 mr = 0 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 31705 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 181 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.6900000 number of grid points assigned charge 17153 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) : 0.6304009 object centre at (A) : -0.4384995 29.36700 15.54300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.2202991E-02 2.0945832E-02 midg,1,midg; midg,igrid,midg -8.9011242E-04 2.5581261E-02 1,midg,midg; igrid,midg,midg 4.2762958E-02 4.8888434E-02 gauss-seidel spectral radius is 0.9985987 estimated iterations to convergence 212 setup time was (sec) 0.8700000 now iterating at: 22:35:42 rms-change max change #iterations 3.867014 175.2282 at 10iterations 1.782892 67.05482 at 20iterations 0.8249654 30.00620 at 30iterations 0.3811683 13.84240 at 40iterations 0.1760575 6.109126 at 50iterations 8.1646509E-02 2.741495 at 60iterations 3.7853215E-02 1.202479 at 70iterations 1.7552726E-02 0.6026745 at 80iterations 8.0922516E-03 0.2706385 at 90iterations 3.7578519E-03 0.1256409 at 100iterations 1.7499216E-03 6.2229633E-02 at 110iterations 8.1454567E-04 2.8652191E-02 at 120iterations finished qdiffx linear iterations at : 22:35:48 total time elapsed so far: 6.930000 # loops : 120 mean,max change (kT/e) : 8.1454567E-04 2.8652191E-02 energy calculations done at 6.930000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.100000 DelPhi exited at 22:35:49 7.100u 0.225s 0:07.66 95.5% 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 22:35:49 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: 283 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2316 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: 2.836804 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): -27.07400 26.19700 ymin,ymax (A): 8.148999 50.58500 zmin,zma (A): -12.69300 43.77900 x,y,z range (A): 53.27100 42.43600 56.47200 scale (grids/A): 2.836804 object centre (A): -0.4384995 29.36700 15.54300 number of atom coordinates read : 2316 total number of charged atoms : 2182 net assigned charge : 11.50003 assigned positive charge : 338.3774 centred at (gu) : 92.87077 96.17751 93.84194 assigned negative charge : -326.8781 centred at (gu) : 93.00486 95.94436 93.85184 start vw surface at 0.1800000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 157006 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22487 grid for indexing accessible points = 1.400000 m= 78028 mr = 110105 m= 28335 mr = 62086 m= 6832 mr = 22059 m= 953 mr = 4876 m= 56 mr = 578 m= 2 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.7100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.250000 number of dielectric boundary points 71498 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2 iepsmp to db, and charging done at 1.390000 number of grid points assigned charge 17455 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) : 1.891203 object centre at (A) : -0.4384995 29.36700 15.54300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5963129 0.1848223 midg,1,midg; midg,igrid,midg -1.8481592E-02 0.2778212 1,midg,midg; igrid,midg,midg 0.4600397 0.4448151 gauss-seidel spectral radius is 0.9992539 estimated iterations to convergence 289 setup time was (sec) 1.540000 now iterating at: 22:35:51 rms-change max change #iterations 9.223579 358.9473 at 10iterations 5.431605 151.6470 at 20iterations 3.160161 67.35464 at 30iterations 1.838670 42.40910 at 40iterations 1.066596 26.42622 at 50iterations 0.6175605 13.85314 at 60iterations 0.3558832 7.959013 at 70iterations 0.2050500 4.114349 at 80iterations 0.1181706 2.309655 at 90iterations 6.8083681E-02 1.398022 at 100iterations 3.9135620E-02 0.8719282 at 110iterations 2.2475993E-02 0.5004940 at 120iterations 1.2945424E-02 0.2596431 at 130iterations 7.4126353E-03 0.1538134 at 140iterations 4.2610946E-03 8.5733414E-02 at 150iterations 2.4519807E-03 4.6520233E-02 at 160iterations 1.4099934E-03 2.8480530E-02 at 170iterations 8.1597589E-04 1.5564919E-02 at 180iterations finished qdiffx linear iterations at : 22:36:00 total time elapsed so far: 11.13000 # loops : 180 mean,max change (kT/e) : 8.1597589E-04 1.5564919E-02 energy calculations done at 11.13000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.30000 DelPhi exited at 22:36:01 11.301u 0.228s 0:11.80 97.6% 0+0k 0+0io 0pf+0w