Sat Oct 8 11:36:30 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 11:36:31 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 = 3345 !!! WARNING: HIR 14 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6354193 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): 31.32400 82.00300 ymin,ymax (A): 24.65800 80.68400 zmin,zma (A): -3.306000 46.05200 x,y,z range (A): 50.67900 56.02600 49.35800 scale (grids/A): 0.6354193 object centre (A): 56.66350 52.67100 21.37300 number of atom coordinates read : 3345 total number of charged atoms : 3193 net assigned charge : -5.485962 assigned positive charge : 509.7534 centred at (gu) : 90.31296 89.55879 91.32138 assigned negative charge : -515.2404 centred at (gu) : 90.13415 89.63958 91.32793 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8541 nv = 96 ne = 84 npr = 72302 no. pairs analyzed = 72302 no. exposed pairs = 3614 no. arc points = 24683 no. surface atoms = 1231 nbur = 2114 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 468 mr = 5134 m= 0 mr = 75 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 186 time to turn everything in is 0.3500000 number of dielectric boundary points 3800 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2484 ## 238 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 10749 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.7220641E-09 -1.0539802E-08 midg,1,midg; midg,igrid,midg 4.2685131E-09 -1.6551379E-08 1,midg,midg; igrid,midg,midg -2.9851709E-08 1.8053740E-08 gauss-seidel spectral radius is 0.9872174 estimated iterations to convergence 72 setup time was (sec) 0.6200000 now iterating at: 11:36:31 rms-change max change #iterations 0.1683337 24.05344 at 10iterations 1.6377607E-02 2.280869 at 20iterations 1.6259419E-03 0.2199150 at 30iterations 1.6035781E-04 1.9176483E-02 at 40iterations 1.5767542E-05 2.2487640E-03 at 50iterations finished qdiffx linear iterations at : 11:36:35 total time elapsed so far: 4.090000 # loops : 50 mean,max change (kT/e) : 1.5767542E-05 2.2487640E-03 energy calculations done at 4.090000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.270000 DelPhi exited at 11:36:36 4.269u 0.253s 0:05.01 90.0% 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 Sat Oct 8 2011 at 11:36:36 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 = 3345 !!! WARNING: HIR 14 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= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.906258 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): 31.32400 82.00300 ymin,ymax (A): 24.65800 80.68400 zmin,zma (A): -3.306000 46.05200 x,y,z range (A): 50.67900 56.02600 49.35800 scale (grids/A): 1.906258 object centre (A): 56.66350 52.67100 21.37300 number of atom coordinates read : 3345 total number of charged atoms : 3193 net assigned charge : -5.485962 assigned positive charge : 509.7534 centred at (gu) : 90.93847 88.67580 93.96295 assigned negative charge : -515.2404 centred at (gu) : 90.40195 88.91829 93.98333 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 93138 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24683 grid for indexing accessible points = 1.400000 m= 34939 mr = 68001 m= 5751 mr = 27130 m= 337 mr = 3961 m= 5 mr = 141 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 8130 time to turn everything in is 0.6700000 number of dielectric boundary points 34937 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 159 iepsmp to db, and charging done at 0.8000000 number of grid points assigned charge 25117 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) : 0.6354193 object centre at (A) : 56.66350 52.67100 21.37300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.4177416E-02 -3.8002074E-02 midg,1,midg; midg,igrid,midg 1.3242254E-02 -3.0301075E-02 1,midg,midg; igrid,midg,midg -4.8513237E-02 7.2050551E-03 gauss-seidel spectral radius is 0.9986875 estimated iterations to convergence 219 setup time was (sec) 0.9900000 now iterating at: 11:36:37 rms-change max change #iterations 4.977925 206.9955 at 10iterations 2.361897 66.16183 at 20iterations 1.126173 30.40121 at 30iterations 0.5359151 14.30835 at 40iterations 0.2549919 7.655521 at 50iterations 0.1215415 3.483599 at 60iterations 5.7895035E-02 1.777430 at 70iterations 2.7611641E-02 0.7596569 at 80iterations 1.3126882E-02 0.3757553 at 90iterations 6.2673008E-03 0.1877193 at 100iterations 2.9793074E-03 8.4291458E-02 at 110iterations 1.4214048E-03 4.1215897E-02 at 120iterations finished qdiffx linear iterations at : 11:36:46 total time elapsed so far: 9.780000 # loops : 120 mean,max change (kT/e) : 1.4214048E-03 4.1215897E-02 energy calculations done at 9.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.960000 DelPhi exited at 11:36:46 9.966u 0.291s 0:10.77 95.1% 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 Sat Oct 8 2011 at 11:36:46 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 = 3345 !!! WARNING: HIR 14 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.859387 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): 31.32400 82.00300 ymin,ymax (A): 24.65800 80.68400 zmin,zma (A): -3.306000 46.05200 x,y,z range (A): 50.67900 56.02600 49.35800 scale (grids/A): 2.859387 object centre (A): 56.66350 52.67100 21.37300 number of atom coordinates read : 3345 total number of charged atoms : 3193 net assigned charge : -5.485962 assigned positive charge : 509.7534 centred at (gu) : 91.40749 88.01322 95.94401 assigned negative charge : -515.2404 centred at (gu) : 90.60275 88.37723 95.97488 start vw surface at 0.1600000 fill in re-entrant regions at 0.6000000 boundary points on vw surface= 215626 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24683 grid for indexing accessible points = 1.400000 m= 112069 mr = 163955 m= 42454 mr = 94390 m= 10519 mr = 35774 m= 1590 mr = 8355 m= 133 mr = 1149 m= 1 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 28456 time to turn everything in is 1.780000 number of dielectric boundary points 78696 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.930000 number of grid points assigned charge 25544 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) : 1.906258 object centre at (A) : 56.66350 52.67100 21.37300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1516999 -0.3429927 midg,1,midg; midg,igrid,midg 0.1792063 -0.2687725 1,midg,midg; igrid,midg,midg -0.4899147 9.3844244E-03 gauss-seidel spectral radius is 0.9992728 estimated iterations to convergence 293 setup time was (sec) 2.130000 now iterating at: 11:36:49 rms-change max change #iterations 11.37795 447.2236 at 10iterations 6.592210 123.9188 at 20iterations 3.821631 61.46490 at 30iterations 2.202406 34.62149 at 40iterations 1.273861 23.19971 at 50iterations 0.7358738 12.24944 at 60iterations 0.4248808 7.034964 at 70iterations 0.2449214 4.142767 at 80iterations 0.1417428 2.189944 at 90iterations 8.1645168E-02 1.355276 at 100iterations 4.7114350E-02 0.7120972 at 110iterations 2.7208978E-02 0.4372334 at 120iterations 1.5697058E-02 0.2487602 at 130iterations 9.0735424E-03 0.1415443 at 140iterations 5.2263699E-03 8.2428932E-02 at 150iterations 3.0162893E-03 4.8216343E-02 at 160iterations 1.7436317E-03 2.8462410E-02 at 170iterations 1.0074580E-03 1.6441345E-02 at 180iterations finished qdiffx linear iterations at : 11:37:03 total time elapsed so far: 15.93000 # loops : 180 mean,max change (kT/e) : 1.0074580E-03 1.6441345E-02 energy calculations done at 15.93000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.11000 DelPhi exited at 11:37:03 16.115u 0.283s 0:16.71 98.0% 0+0k 0+0io 0pf+0w