Tue Oct 11 05:14:12 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 Tue Oct 11 2011 at 05:14:12 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2247 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6784570 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): 1.506000 46.68800 ymin,ymax (A): 0.5820001 41.57000 zmin,zma (A): -2.435000 50.03700 x,y,z range (A): 45.18200 40.98800 52.47200 scale (grids/A): 0.6784570 object centre (A): 24.09700 21.07600 23.80100 number of atom coordinates read : 2247 total number of charged atoms : 1943 net assigned charge : 6.931010 assigned positive charge : 315.1771 centred at (gu) : 90.79240 90.22666 89.49414 assigned negative charge : -308.2461 centred at (gu) : 90.96991 90.21378 89.52505 start vw surface at 0.1500000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 6418 nv = 96 ne = 84 npr = 40567 no. pairs analyzed = 40567 no. exposed pairs = 2550 no. arc points = 17346 no. surface atoms = 869 nbur = 1378 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 405 mr = 3617 m= 2 mr = 50 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 0.3100000 number of dielectric boundary points 3158 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1697 ## 144 charges are in solution ## iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 7377 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 4.0559684E-08 1.9345109E-08 midg,1,midg; midg,igrid,midg 2.4699025E-08 3.3691013E-08 1,midg,midg; igrid,midg,midg 6.1693520E-08 -1.9155607E-08 gauss-seidel spectral radius is 0.9886831 estimated iterations to convergence 77 setup time was (sec) 0.5700000 now iterating at: 05:14:13 rms-change max change #iterations 0.1671434 26.78371 at 10iterations 1.8901778E-02 3.045242 at 20iterations 2.5069662E-03 0.3723679 at 30iterations 4.3718022E-04 6.0798645E-02 at 40iterations 1.1034403E-04 1.2619019E-02 at 50iterations finished qdiffx linear iterations at : 05:14:17 total time elapsed so far: 3.880000 # loops : 50 mean,max change (kT/e) : 1.1034403E-04 1.2619019E-02 energy calculations done at 3.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.050000 DelPhi exited at 05:14:17 4.051u 0.265s 0:04.80 89.7% 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 Tue Oct 11 2011 at 05:14:17 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2247 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.035371 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): 1.506000 46.68800 ymin,ymax (A): 0.5820001 41.57000 zmin,zma (A): -2.435000 50.03700 x,y,z range (A): 45.18200 40.98800 52.47200 scale (grids/A): 2.035371 object centre (A): 24.09700 21.07600 23.80100 number of atom coordinates read : 2247 total number of charged atoms : 1943 net assigned charge : 6.931010 assigned positive charge : 315.1771 centred at (gu) : 92.37708 90.67964 88.48239 assigned negative charge : -308.2461 centred at (gu) : 92.90981 90.64147 88.57510 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 68425 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17346 grid for indexing accessible points = 1.400000 m= 27173 mr = 48343 m= 4950 mr = 20349 m= 373 mr = 3207 m= 7 mr = 138 m= 0 mr = 2 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 28889 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 97 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 15384 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) : 0.6784570 object centre at (A) : 24.09700 21.07600 23.80100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.6631459E-02 5.4111455E-02 midg,1,midg; midg,igrid,midg 3.6274558E-03 2.1605456E-02 1,midg,midg; igrid,midg,midg 3.4186095E-02 -3.0745745E-03 gauss-seidel spectral radius is 0.9987394 estimated iterations to convergence 223 setup time was (sec) 0.9300000 now iterating at: 05:14:18 rms-change max change #iterations 4.202998 186.4077 at 10iterations 2.041719 64.60143 at 20iterations 0.9869690 31.41544 at 30iterations 0.4750462 15.96284 at 40iterations 0.2306856 7.381798 at 50iterations 0.1117621 3.619987 at 60iterations 5.4077450E-02 1.803053 at 70iterations 2.6271803E-02 0.9518452 at 80iterations 1.2819037E-02 0.3979750 at 90iterations 6.3020298E-03 0.2125803 at 100iterations 3.1453390E-03 9.7043037E-02 at 110iterations 1.6250217E-03 5.1504612E-02 at 120iterations finished qdiffx linear iterations at : 05:14:27 total time elapsed so far: 9.190000 # loops : 120 mean,max change (kT/e) : 1.6250217E-03 5.1504612E-02 energy calculations done at 9.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.360000 DelPhi exited at 05:14:28 9.359u 0.297s 0:10.26 93.9% 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 Tue Oct 11 2011 at 05:14:28 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: 296 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2247 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.053057 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): 1.506000 46.68800 ymin,ymax (A): 0.5820001 41.57000 zmin,zma (A): -2.435000 50.03700 x,y,z range (A): 45.18200 40.98800 52.47200 scale (grids/A): 3.053057 object centre (A): 24.09700 21.07600 23.80100 number of atom coordinates read : 2247 total number of charged atoms : 1943 net assigned charge : 6.931010 assigned positive charge : 315.1771 centred at (gu) : 93.56574 91.01952 87.72359 assigned negative charge : -308.2461 centred at (gu) : 94.36459 90.96210 87.86271 start vw surface at 0.1500000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 157669 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17346 grid for indexing accessible points = 1.400000 m= 85045 mr = 116497 m= 33688 mr = 70306 m= 9150 mr = 27412 m= 1591 mr = 6932 m= 132 mr = 1109 m= 5 mr = 71 m= 0 mr = 2 time to grow re-entrant surface = 1.000000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.660000 number of dielectric boundary points 64951 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 15544 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) : 2.035371 object centre at (A) : 24.09700 21.07600 23.80100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3542454 0.7781245 midg,1,midg; midg,igrid,midg 5.1357606E-03 0.1912021 1,midg,midg; igrid,midg,midg 0.2777297 2.3949241E-02 gauss-seidel spectral radius is 0.9992722 estimated iterations to convergence 293 setup time was (sec) 1.990000 now iterating at: 05:14:30 rms-change max change #iterations 9.691771 358.8784 at 10iterations 5.681798 125.9654 at 20iterations 3.339110 75.94736 at 30iterations 1.950487 42.47800 at 40iterations 1.138106 26.27304 at 50iterations 0.6639643 14.90487 at 60iterations 0.3863088 7.814041 at 70iterations 0.2247470 4.135722 at 80iterations 0.1304290 2.742491 at 90iterations 7.6069407E-02 1.545672 at 100iterations 4.4257399E-02 0.8595276 at 110iterations 2.5889887E-02 0.5565243 at 120iterations 1.5286987E-02 0.2924118 at 130iterations 9.1691716E-03 0.1814804 at 140iterations 5.6182351E-03 0.1230240 at 150iterations 3.5979243E-03 7.1842194E-02 at 160iterations 2.4324493E-03 4.6974182E-02 at 170iterations 1.7352059E-03 3.3935547E-02 at 180iterations finished qdiffx linear iterations at : 05:14:43 total time elapsed so far: 15.51000 # loops : 180 mean,max change (kT/e) : 1.7352059E-03 3.3935547E-02 energy calculations done at 15.51000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.68000 DelPhi exited at 05:14:44 15.683u 0.309s 0:16.49 96.9% 0+0k 0+0io 0pf+0w