Wed Feb 15 08:56:42 PST 2012 #!/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_thinner.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 Wed Feb 15 2012 at 08:56:42 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 ! Automatically converted by prot2crg.py # of charge parameter records: 959 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3045 !!! WARNING: DIC 117 has a net charge of -0.8000 !!! WARNING: DID 121 has a net charge of -0.8000 !!! WARNING: DID 257 has a net charge of -0.8000 !!! WARNING: MG9 970 has a net charge of 1.8000 !!! WARNING: MG9 971 has a net charge of 1.8000 !!! WARNING: MG9 972 has a net charge of 1.8000 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: 0.6294090 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): -15.75500 37.01100 ymin,ymax (A): 3.380000 56.65500 zmin,zma (A): -34.64800 21.91300 x,y,z range (A): 52.76600 53.27500 56.56100 scale (grids/A): 0.6294090 object centre (A): 10.62800 30.01750 -6.367499 number of atom coordinates read : 3045 total number of charged atoms : 2901 net assigned charge : 4.500014 assigned positive charge : 456.2972 centred at (gu) : 90.51463 91.41674 88.64815 assigned negative charge : -451.7987 centred at (gu) : 90.54946 91.51427 88.59501 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8028 nv = 96 ne = 84 npr = 62925 no. pairs analyzed = 62925 no. exposed pairs = 3813 no. arc points = 26840 no. surface atoms = 1282 nbur = 1763 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 489 mr = 4400 m= 4 mr = 61 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4000000 number of dielectric boundary points 4060 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2599 ## 253 charges are in solution ## iepsmp to db, and charging done at 0.5000000 number of grid points assigned charge 9855 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.5648197E-10 7.7667250E-09 midg,1,midg; midg,igrid,midg 1.0884490E-08 -6.8161006E-09 1,midg,midg; igrid,midg,midg 7.6564568E-09 1.6819280E-09 gauss-seidel spectral radius is 0.9869643 estimated iterations to convergence 72 setup time was (sec) 0.6300000 now iterating at: 08:56:43 rms-change max change #iterations 0.1529279 24.24219 at 10iterations 1.6511381E-02 2.001411 at 20iterations 3.1529232E-03 0.4564209 at 30iterations 1.1087040E-03 0.1562099 at 40iterations 4.4010885E-04 6.6392899E-02 at 50iterations finished qdiffx linear iterations at : 08:56:46 total time elapsed so far: 3.290000 # loops : 50 mean,max change (kT/e) : 4.4010885E-04 6.6392899E-02 energy calculations done at 3.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.480000 DelPhi exited at 08:56:46 3.484u 0.137s 0:04.03 89.5% 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 Wed Feb 15 2012 at 08:56:46 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 ! Automatically converted by prot2crg.py # of charge parameter records: 959 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3045 !!! WARNING: DIC 117 has a net charge of -0.8000 !!! WARNING: DID 121 has a net charge of -0.8000 !!! WARNING: DID 257 has a net charge of -0.8000 !!! WARNING: MG9 970 has a net charge of 1.8000 !!! WARNING: MG9 971 has a net charge of 1.8000 !!! WARNING: MG9 972 has a net charge of 1.8000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 1.888227 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): -15.75500 37.01100 ymin,ymax (A): 3.380000 56.65500 zmin,zma (A): -34.64800 21.91300 x,y,z range (A): 52.76600 53.27500 56.56100 scale (grids/A): 1.888227 object centre (A): 10.62800 30.01750 -6.367499 number of atom coordinates read : 3045 total number of charged atoms : 2901 net assigned charge : 4.500014 assigned positive charge : 456.2972 centred at (gu) : 91.54322 94.24958 85.94362 assigned negative charge : -451.7987 centred at (gu) : 91.64826 94.54284 85.78500 start vw surface at 0.2000000 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 86831 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26840 grid for indexing accessible points = 1.400000 m= 31246 mr = 60228 m= 5114 mr = 22682 m= 285 mr = 3000 m= 4 mr = 89 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.7100000 number of dielectric boundary points 37481 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 162 iepsmp to db, and charging done at 0.8400000 number of grid points assigned charge 22754 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) : 0.6294090 object centre at (A) : 10.62800 30.01750 -6.367499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.6921172E-02 2.6546903E-02 midg,1,midg; midg,igrid,midg -3.7604785E-03 -6.7167915E-03 1,midg,midg; igrid,midg,midg -3.2248849E-03 -3.6241822E-03 gauss-seidel spectral radius is 0.9986523 estimated iterations to convergence 216 setup time was (sec) 1.030000 now iterating at: 08:56:48 rms-change max change #iterations 4.635729 186.4091 at 10iterations 2.176450 80.00031 at 20iterations 1.027507 32.05725 at 30iterations 0.4825527 14.25722 at 40iterations 0.2288333 7.163376 at 50iterations 0.1075814 3.318270 at 60iterations 5.0940633E-02 1.565689 at 70iterations 2.4448834E-02 0.8606796 at 80iterations 1.1902257E-02 0.3483124 at 90iterations 6.0975477E-03 0.1845093 at 100iterations 3.3277462E-03 0.1083355 at 110iterations 1.9766698E-03 6.8431854E-02 at 120iterations finished qdiffx linear iterations at : 08:56:55 total time elapsed so far: 8.140000 # loops : 120 mean,max change (kT/e) : 1.9766698E-03 6.8431854E-02 energy calculations done at 8.140000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.340000 DelPhi exited at 08:56:55 8.339u 0.260s 0:09.00 95.4% 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 Wed Feb 15 2012 at 08:56:55 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 ! Automatically converted by prot2crg.py # of charge parameter records: 959 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3045 !!! WARNING: DIC 117 has a net charge of -0.8000 !!! WARNING: DID 121 has a net charge of -0.8000 !!! WARNING: DID 257 has a net charge of -0.8000 !!! WARNING: MG9 970 has a net charge of 1.8000 !!! WARNING: MG9 971 has a net charge of 1.8000 !!! WARNING: MG9 972 has a net charge of 1.8000 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: 2.832340 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): -15.75500 37.01100 ymin,ymax (A): 3.380000 56.65500 zmin,zma (A): -34.64800 21.91300 x,y,z range (A): 52.76600 53.27500 56.56100 scale (grids/A): 2.832340 object centre (A): 10.62800 30.01750 -6.367499 number of atom coordinates read : 3045 total number of charged atoms : 2901 net assigned charge : 4.500014 assigned positive charge : 456.2972 centred at (gu) : 92.31475 96.37411 83.91539 assigned negative charge : -451.7987 centred at (gu) : 92.47249 96.81435 83.67750 start vw surface at 0.1800000 fill in re-entrant regions at 0.5600000 boundary points on vw surface= 201428 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26840 grid for indexing accessible points = 1.400000 m= 100613 mr = 146867 m= 36973 mr = 81367 m= 9135 mr = 29283 m= 1269 mr = 6654 m= 67 mr = 774 m= 3 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 1.010000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.710000 number of dielectric boundary points 84520 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.870000 number of grid points assigned charge 23207 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) : 1.888227 object centre at (A) : 10.62800 30.01750 -6.367499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2417955 0.4119387 midg,1,midg; midg,igrid,midg -0.2091455 -5.9857111E-02 1,midg,midg; igrid,midg,midg -0.1335928 -1.2497375E-02 gauss-seidel spectral radius is 0.9992748 estimated iterations to convergence 293 setup time was (sec) 2.040000 now iterating at: 08:56:58 rms-change max change #iterations 10.92883 373.4799 at 10iterations 6.458379 168.8418 at 20iterations 3.787044 82.06698 at 30iterations 2.219976 44.24483 at 40iterations 1.294407 26.91479 at 50iterations 0.7550792 14.88091 at 60iterations 0.4394587 8.440289 at 70iterations 0.2552107 5.242712 at 80iterations 0.1487708 2.741299 at 90iterations 8.6208232E-02 1.477198 at 100iterations 5.0200965E-02 0.8746214 at 110iterations 2.9271863E-02 0.5030212 at 120iterations 1.7214168E-02 0.3181229 at 130iterations 1.0266225E-02 0.1857681 at 140iterations 6.2915282E-03 0.1246338 at 150iterations 4.0330659E-03 7.7615738E-02 at 160iterations 2.7192433E-03 5.8677673E-02 at 170iterations 1.9714646E-03 3.8208008E-02 at 180iterations finished qdiffx linear iterations at : 08:57:10 total time elapsed so far: 14.23000 # loops : 180 mean,max change (kT/e) : 1.9714646E-03 3.8208008E-02 energy calculations done at 14.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.42000 DelPhi exited at 08:57:10 14.426u 0.224s 0:14.98 97.7% 0+0k 0+0io 0pf+0w