Mon Oct 10 16:04:26 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+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 Mon Oct 10 2011 at 16:04:26 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 # of charge parameter records: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4290 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ZN9 979 has a net charge of 1.4000 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: 0.5492217 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): 7.375000 58.97300 ymin,ymax (A): -29.58500 34.30400 zmin,zma (A): -29.24700 35.57200 x,y,z range (A): 51.59800 63.88900 64.81900 scale (grids/A): 0.5492217 object centre (A): 33.17400 2.359501 3.162501 number of atom coordinates read : 4290 total number of charged atoms : 4187 net assigned charge : 7.700025 assigned positive charge : 648.3138 centred at (gu) : 89.83226 89.60236 88.73886 assigned negative charge : -640.6174 centred at (gu) : 89.80760 89.57629 88.75032 start vw surface at 0.1900000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 8488 nv = 96 ne = 84 npr = 86327 no. pairs analyzed = 86327 no. exposed pairs = 5309 no. arc points = 36263 no. surface atoms = 1790 nbur = 2500 mkacc time = 0.1900000 writing accessible surface arcs data to file ARCDAT initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.568000 m= 339 mr = 4642 m= 0 mr = 16 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 12 time to turn everything in is 0.4200000 number of dielectric boundary points 4169 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3708 ## 456 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 11185 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.0502977E-10 3.1217942E-10 midg,1,midg; midg,igrid,midg 2.8533512E-10 7.4763612E-10 1,midg,midg; igrid,midg,midg 2.8683547E-10 7.7590012E-10 gauss-seidel spectral radius is 0.9830035 estimated iterations to convergence 63 setup time was (sec) 0.6500000 now iterating at: 16:04:27 rms-change max change #iterations 9.2348516E-02 13.07477 at 10iterations 6.5178592E-03 0.9413004 at 20iterations 5.8668078E-04 9.2134476E-02 at 30iterations 1.1850168E-04 2.0235062E-02 at 40iterations 3.6266796E-05 4.8122406E-03 at 50iterations finished qdiffx linear iterations at : 16:04:29 total time elapsed so far: 3.230000 # loops : 50 mean,max change (kT/e) : 3.6266796E-05 4.8122406E-03 energy calculations done at 3.230000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 16:04:30 3.411u 0.150s 0:03.84 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 Mon Oct 10 2011 at 16:04:30 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4290 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ZN9 979 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1500000 grid size : 179 scale,in grids/A, set to be: 1.647665 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): 7.375000 58.97300 ymin,ymax (A): -29.58500 34.30400 zmin,zma (A): -29.24700 35.57200 x,y,z range (A): 51.59800 63.88900 64.81900 scale (grids/A): 1.647665 object centre (A): 33.17400 2.359501 3.162501 number of atom coordinates read : 4290 total number of charged atoms : 4187 net assigned charge : 7.700025 assigned positive charge : 648.3138 centred at (gu) : 89.49541 88.80564 86.21499 assigned negative charge : -640.6174 centred at (gu) : 89.42216 88.72829 86.25055 start vw surface at 0.2400000 fill in re-entrant regions at 0.3600000 boundary points on vw surface= 94462 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36263 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 30678 mr = 66761 m= 3442 mr = 21356 m= 94 mr = 1757 m= 0 mr = 10 time to grow re-entrant surface = 0.3000000 no. cavity mid-points inaccessible to solvent = 572 time to turn everything in is 0.7000000 number of dielectric boundary points 38792 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 411 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 32150 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) : 0.5492217 object centre at (A) : 33.17400 2.359501 3.162501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.7095875E-02 -2.8749297E-03 midg,1,midg; midg,igrid,midg 1.7204501E-02 1.7945483E-02 1,midg,midg; igrid,midg,midg 3.8799152E-03 2.4875407E-03 gauss-seidel spectral radius is 0.9983547 estimated iterations to convergence 196 setup time was (sec) 1.000000 now iterating at: 16:04:31 rms-change max change #iterations 4.191581 156.5219 at 10iterations 1.821113 56.87329 at 20iterations 0.7949105 24.66354 at 30iterations 0.3466772 10.19553 at 40iterations 0.1508321 4.364346 at 50iterations 6.5775454E-02 2.119954 at 60iterations 2.8860131E-02 0.8734932 at 70iterations 1.2586893E-02 0.3789177 at 80iterations 5.4942621E-03 0.1640625 at 90iterations 2.4158107E-03 7.7102661E-02 at 100iterations 1.0661853E-03 3.1520844E-02 at 110iterations 4.7684700E-04 1.4570713E-02 at 120iterations finished qdiffx linear iterations at : 16:04:38 total time elapsed so far: 7.630000 # loops : 120 mean,max change (kT/e) : 4.7684700E-04 1.4570713E-02 energy calculations done at 7.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.800000 DelPhi exited at 16:04:38 7.807u 0.239s 0:08.36 96.0% 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 Mon Oct 10 2011 at 16:04:38 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: 259 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4290 !!! WARNING: HIZ 295 has a net charge of 0.2000 !!! WARNING: HIZ 299 has a net charge of 0.2000 !!! WARNING: GLM 318 has a net charge of -0.6000 !!! WARNING: ZN9 979 has a net charge of 1.4000 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: 2.471498 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): 7.375000 58.97300 ymin,ymax (A): -29.58500 34.30400 zmin,zma (A): -29.24700 35.57200 x,y,z range (A): 51.59800 63.88900 64.81900 scale (grids/A): 2.471498 object centre (A): 33.17400 2.359501 3.162501 number of atom coordinates read : 4290 total number of charged atoms : 4187 net assigned charge : 7.700025 assigned positive charge : 648.3138 centred at (gu) : 89.24262 88.20811 84.32213 assigned negative charge : -640.6174 centred at (gu) : 89.13300 88.09228 84.37584 start vw surface at 0.1900000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 220007 reading accessible surface arcs data from file ARCDAT no. of arc points read = 36263 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 105332 mr = 163600 m= 31204 mr = 83769 m= 5502 mr = 23708 m= 465 mr = 3667 m= 10 mr = 203 m= 0 mr = 0 time to grow re-entrant surface = 0.9400001 no. cavity mid-points inaccessible to solvent = 1948 time to turn everything in is 1.600000 number of dielectric boundary points 87573 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 25 iepsmp to db, and charging done at 1.740000 number of grid points assigned charge 33456 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) : 1.647665 object centre at (A) : 33.17400 2.359501 3.162501 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4289086 -8.0183722E-02 midg,1,midg; midg,igrid,midg 0.3308866 0.2311254 1,midg,midg; igrid,midg,midg 5.1183339E-02 3.5889529E-02 gauss-seidel spectral radius is 0.9992253 estimated iterations to convergence 284 setup time was (sec) 1.910000 now iterating at: 16:04:40 rms-change max change #iterations 10.82372 314.5833 at 10iterations 6.343088 182.5310 at 20iterations 3.695757 83.50209 at 30iterations 2.147555 46.98773 at 40iterations 1.239960 23.94560 at 50iterations 0.7141721 15.33744 at 60iterations 0.4110777 7.407552 at 70iterations 0.2357234 4.300121 at 80iterations 0.1351049 2.403126 at 90iterations 7.7090561E-02 1.309694 at 100iterations 4.3985061E-02 0.8417473 at 110iterations 2.5140116E-02 0.4278889 at 120iterations 1.4363083E-02 0.2397022 at 130iterations 8.1985537E-03 0.1382904 at 140iterations 4.6762200E-03 8.8984966E-02 at 150iterations 2.6815513E-03 4.5952797E-02 at 160iterations 1.5438709E-03 2.9800415E-02 at 170iterations 8.9668832E-04 1.6951561E-02 at 180iterations finished qdiffx linear iterations at : 16:04:51 total time elapsed so far: 12.86000 # loops : 180 mean,max change (kT/e) : 8.9668832E-04 1.6951561E-02 energy calculations done at 12.86000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.04000 DelPhi exited at 16:04:52 13.039u 0.233s 0:13.65 97.1% 0+0k 0+0io 0pf+0w