Sun Jan 29 18:26:22 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.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 Jan 29 2012 at 18:26:22 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 = 3044 !!! 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= 5.9999999E-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 : 3044 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 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 8091 nv = 96 ne = 84 npr = 62251 no. pairs analyzed = 62251 no. exposed pairs = 3781 no. arc points = 26630 no. surface atoms = 1283 nbur = 1761 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 496 mr = 4488 m= 3 mr = 61 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 0.2300000 number of dielectric boundary points 4041 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2568 ## 248 charges are in solution ## iepsmp to db, and charging done at 0.3000000 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 0.9869648 estimated iterations to convergence 72 setup time was (sec) 0.4300000 now iterating at: 18:26:23 rms-change max change #iterations 0.1541648 22.89043 at 10iterations 1.6109960E-02 2.280205 at 20iterations 2.4453891E-03 0.3725586 at 30iterations 6.7476073E-04 0.1176033 at 40iterations 2.4641730E-04 4.5751572E-02 at 50iterations finished qdiffx linear iterations at : 18:26:26 total time elapsed so far: 3.360000 # loops : 50 mean,max change (kT/e) : 2.4641730E-04 4.5751572E-02 energy calculations done at 3.360000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.500000 DelPhi exited at 18:26:26 3.506u 0.193s 0:03.98 92.7% 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 Sun Jan 29 2012 at 18:26:26 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 = 3044 !!! 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= 5.9999999E-02 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 : 3044 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 0.1000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 87624 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26630 grid for indexing accessible points = 1.400000 m= 31608 mr = 61118 m= 5198 mr = 23103 m= 296 mr = 3102 m= 5 mr = 91 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4400000 number of dielectric boundary points 37317 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 162 iepsmp to db, and charging done at 0.5300000 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 1.7492807E-02 2.5947534E-02 midg,1,midg; midg,igrid,midg -3.6648517E-03 -6.4091426E-03 1,midg,midg; igrid,midg,midg -2.4346709E-03 -3.0132115E-03 gauss-seidel spectral radius is 0.9986523 estimated iterations to convergence 216 setup time was (sec) 0.6700000 now iterating at: 18:26:27 rms-change max change #iterations 4.636225 186.4119 at 10iterations 2.176138 80.00278 at 20iterations 1.027754 31.94294 at 30iterations 0.4816257 13.98448 at 40iterations 0.2285535 7.217110 at 50iterations 0.1073712 3.312277 at 60iterations 5.0517377E-02 1.574219 at 70iterations 2.4029551E-02 0.7354279 at 80iterations 1.1572503E-02 0.3613999 at 90iterations 5.7006017E-03 0.1803169 at 100iterations 2.8755276E-03 0.1012974 at 110iterations 1.5531849E-03 5.2853823E-02 at 120iterations finished qdiffx linear iterations at : 18:26:34 total time elapsed so far: 7.960000 # loops : 120 mean,max change (kT/e) : 1.5531849E-03 5.2853823E-02 energy calculations done at 7.960000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.090000 DelPhi exited at 18:26:35 8.091u 0.212s 0:08.57 96.8% 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 Jan 29 2012 at 18:26:35 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 = 3044 !!! 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= 5.9999999E-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 : 3044 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 0.1000000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 203215 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26630 grid for indexing accessible points = 1.400000 m= 102012 mr = 148842 m= 37466 mr = 82945 m= 9320 mr = 29820 m= 1304 mr = 6869 m= 73 mr = 791 m= 1 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.6500000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.130000 number of dielectric boundary points 84101 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.230000 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 0.2481372 0.4058083 midg,1,midg; midg,igrid,midg -0.2084188 -5.7307120E-02 1,midg,midg; igrid,midg,midg -0.1236517 -7.2630825E-03 gauss-seidel spectral radius is 0.9992733 estimated iterations to convergence 293 setup time was (sec) 1.370000 now iterating at: 18:26:36 rms-change max change #iterations 10.92599 373.2678 at 10iterations 6.447111 154.6634 at 20iterations 3.774838 75.96430 at 30iterations 2.210546 44.75196 at 40iterations 1.286880 26.80857 at 50iterations 0.7495247 13.76678 at 60iterations 0.4359011 7.697272 at 70iterations 0.2527014 5.441259 at 80iterations 0.1471711 3.169800 at 90iterations 8.5192099E-02 1.502697 at 100iterations 4.9445689E-02 0.8373070 at 110iterations 2.8757317E-02 0.4710617 at 120iterations 1.6833954E-02 0.3162689 at 130iterations 9.9373655E-03 0.1798849 at 140iterations 5.9655588E-03 0.1109505 at 150iterations 3.6806876E-03 6.8950653E-02 at 160iterations 2.3671533E-03 5.6987762E-02 at 170iterations 1.6193838E-03 3.3473969E-02 at 180iterations finished qdiffx linear iterations at : 18:26:48 total time elapsed so far: 13.01000 # loops : 180 mean,max change (kT/e) : 1.6193838E-03 3.3473969E-02 energy calculations done at 13.01000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.15000 DelPhi exited at 18:26:48 13.148u 0.219s 0:13.64 97.8% 0+0k 0+0io 0pf+0w