Sun Oct 9 23:36:43 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 Sun Oct 9 2011 at 23:36:43 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3656 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1000000 grid size : 179 scale,in grids/A, set to be: 0.5874296 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): -25.06800 30.87900 ymin,ymax (A): -27.02600 26.59300 zmin,zma (A): -9.301000 51.30200 x,y,z range (A): 55.94700 53.61900 60.60300 scale (grids/A): 0.5874296 object centre (A): 2.905500 -0.2165003 21.00050 number of atom coordinates read : 3656 total number of charged atoms : 3540 net assigned charge : -2.499990 assigned positive charge : 564.8533 centred at (gu) : 89.39904 90.35480 89.94390 assigned negative charge : -567.3561 centred at (gu) : 89.47241 90.43085 89.95737 start vw surface at 0.1800000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 8500 nv = 96 ne = 84 npr = 69175 no. pairs analyzed = 69175 no. exposed pairs = 5190 no. arc points = 37338 no. surface atoms = 1682 nbur = 1974 mkacc time = 0.1600000 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 = 1.456000 m= 398 mr = 4180 m= 2 mr = 20 m= 0 mr = 0 time to grow re-entrant surface = 0.1900000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3800000 number of dielectric boundary points 4700 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3755 ## 412 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 10867 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.3156592E-10 -1.1792192E-09 midg,1,midg; midg,igrid,midg 1.8289450E-09 -3.7614378E-09 1,midg,midg; igrid,midg,midg 2.1921622E-09 -2.9253118E-09 gauss-seidel spectral radius is 0.9851090 estimated iterations to convergence 67 setup time was (sec) 0.6000000 now iterating at: 23:36:44 rms-change max change #iterations 0.1176677 15.62753 at 10iterations 9.4479676E-03 1.293274 at 20iterations 8.5751619E-04 0.1123533 at 30iterations 1.5687263E-04 1.6692519E-02 at 40iterations 5.7204124E-05 5.7296753E-03 at 50iterations finished qdiffx linear iterations at : 23:36:46 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 5.7204124E-05 5.7296753E-03 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.380000 DelPhi exited at 23:36:47 3.386u 0.137s 0:03.90 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 Sun Oct 9 2011 at 23:36:47 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3656 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: 1.762289 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): -25.06800 30.87900 ymin,ymax (A): -27.02600 26.59300 zmin,zma (A): -9.301000 51.30200 x,y,z range (A): 55.94700 53.61900 60.60300 scale (grids/A): 1.762289 object centre (A): 2.905500 -0.2165003 21.00050 number of atom coordinates read : 3656 total number of charged atoms : 3540 net assigned charge : -2.499990 assigned positive charge : 564.8533 centred at (gu) : 88.19601 91.06310 89.83050 assigned negative charge : -567.3561 centred at (gu) : 88.41676 91.29227 89.87188 start vw surface at 0.1900000 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 92755 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37338 grid for indexing accessible points = 1.400000 m= 30101 mr = 61080 m= 3759 mr = 20161 m= 164 mr = 1859 m= 2 mr = 33 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 486 time to turn everything in is 0.6600000 number of dielectric boundary points 43648 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 357 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 27590 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) : 0.5874296 object centre at (A) : 2.905500 -0.2165003 21.00050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -8.2539413E-03 -3.2544993E-02 midg,1,midg; midg,igrid,midg 1.5928790E-02 -1.0721672E-02 1,midg,midg; igrid,midg,midg 9.9525927E-03 -4.5300052E-03 gauss-seidel spectral radius is 0.9985508 estimated iterations to convergence 208 setup time was (sec) 0.9400000 now iterating at: 23:36:48 rms-change max change #iterations 4.512157 170.5345 at 10iterations 2.045886 72.41067 at 20iterations 0.9339780 28.93882 at 30iterations 0.4250481 13.59004 at 40iterations 0.1934329 6.230865 at 50iterations 8.8395923E-02 2.540406 at 60iterations 4.0421478E-02 1.254201 at 70iterations 1.8495025E-02 0.5540428 at 80iterations 8.4461495E-03 0.2698808 at 90iterations 3.8777832E-03 0.1182698 at 100iterations 1.7882828E-03 6.3230515E-02 at 110iterations 8.3182205E-04 2.5936127E-02 at 120iterations finished qdiffx linear iterations at : 23:36:54 total time elapsed so far: 7.370000 # loops : 120 mean,max change (kT/e) : 8.3182205E-04 2.5936127E-02 energy calculations done at 7.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.560000 DelPhi exited at 23:36:55 7.558u 0.169s 0:08.13 94.8% 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 Oct 9 2011 at 23:36:55 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 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3656 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 2.643434 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): -25.06800 30.87900 ymin,ymax (A): -27.02600 26.59300 zmin,zma (A): -9.301000 51.30200 x,y,z range (A): 55.94700 53.61900 60.60300 scale (grids/A): 2.643434 object centre (A): 2.905500 -0.2165003 21.00050 number of atom coordinates read : 3656 total number of charged atoms : 3540 net assigned charge : -2.499990 assigned positive charge : 564.8533 centred at (gu) : 87.29365 91.59433 89.74556 assigned negative charge : -567.3561 centred at (gu) : 87.62517 91.93829 89.80769 start vw surface at 0.2300000 fill in re-entrant regions at 0.5800000 boundary points on vw surface= 214671 reading accessible surface arcs data from file ARCDAT no. of arc points read = 37338 grid for indexing accessible points = 1.400000 m= 101026 mr = 149602 m= 31334 mr = 78508 m= 6138 mr = 22925 m= 709 mr = 3963 m= 35 mr = 394 m= 0 mr = 3 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 1868 time to turn everything in is 1.680000 number of dielectric boundary points 98518 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 11 iepsmp to db, and charging done at 1.820000 number of grid points assigned charge 28310 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) : 1.762289 object centre at (A) : 2.905500 -0.2165003 21.00050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1182278 -0.4856447 midg,1,midg; midg,igrid,midg 0.2037961 -0.1255301 1,midg,midg; igrid,midg,midg 9.4612569E-02 -1.3062637E-02 gauss-seidel spectral radius is 0.9992835 estimated iterations to convergence 295 setup time was (sec) 1.990000 now iterating at: 23:36:57 rms-change max change #iterations 11.39800 332.9804 at 10iterations 6.933137 177.9298 at 20iterations 4.175016 94.15489 at 30iterations 2.490581 47.58390 at 40iterations 1.478284 29.58136 at 50iterations 0.8759192 19.18330 at 60iterations 0.5158501 10.81717 at 70iterations 0.3030563 5.756281 at 80iterations 0.1784132 3.396736 at 90iterations 0.1046302 1.995163 at 100iterations 6.1146639E-02 1.100746 at 110iterations 3.5761274E-02 0.6197891 at 120iterations 2.0853691E-02 0.4029465 at 130iterations 1.2189110E-02 0.2102509 at 140iterations 7.1092569E-03 0.1267195 at 150iterations 4.1526915E-03 8.2099915E-02 at 160iterations 2.4190827E-03 4.3738365E-02 at 170iterations 1.4156557E-03 2.7549744E-02 at 180iterations finished qdiffx linear iterations at : 23:37:08 total time elapsed so far: 12.40000 # loops : 180 mean,max change (kT/e) : 1.4156557E-03 2.7549744E-02 energy calculations done at 12.40000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.60000 DelPhi exited at 23:37:08 12.601u 0.172s 0:13.05 97.8% 0+0k 0+0io 0pf+0w