Sat Oct 8 11:37:17 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 Sat Oct 8 2011 at 11:37:18 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 = 4669 !!! WARNING: ALA 536 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 0.5537839 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): -27.24900 35.12900 ymin,ymax (A): 33.77600 98.06100 zmin,zma (A): 30.58900 89.96600 x,y,z range (A): 62.37800 64.28500 59.37700 scale (grids/A): 0.5537839 object centre (A): 3.939999 65.91850 60.27750 number of atom coordinates read : 4669 total number of charged atoms : 4506 net assigned charge : -7.771962 assigned positive charge : 702.5123 centred at (gu) : 90.61520 88.91911 88.94625 assigned negative charge : -710.2883 centred at (gu) : 90.52157 88.95657 89.10127 start vw surface at 0.1200000 fill in re-entrant regions at 0.1200000 boundary points on vw surface= 8957 nv = 96 ne = 84 npr = 98184 no. pairs analyzed = 98184 no. exposed pairs = 5280 no. arc points = 35884 no. surface atoms = 1803 nbur = 2866 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 = 1.540000 m= 370 mr = 5121 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 67 time to turn everything in is 0.3100000 number of dielectric boundary points 4186 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3740 ## 496 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 12093 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.9071185E-09 -2.2601181E-09 midg,1,midg; midg,igrid,midg -2.0461778E-10 -9.4294583E-10 1,midg,midg; igrid,midg,midg -1.7470217E-09 7.2407630E-10 gauss-seidel spectral radius is 0.9833001 estimated iterations to convergence 64 setup time was (sec) 0.5200000 now iterating at: 11:37:18 rms-change max change #iterations 9.9431805E-02 14.14972 at 10iterations 7.4665020E-03 0.9666439 at 20iterations 7.7596289E-04 0.1208382 at 30iterations 1.6855208E-04 2.2815704E-02 at 40iterations 5.3745876E-05 7.5535774E-03 at 50iterations finished qdiffx linear iterations at : 11:37:21 total time elapsed so far: 3.540000 # loops : 50 mean,max change (kT/e) : 5.3745876E-05 7.5535774E-03 energy calculations done at 3.540000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.680000 DelPhi exited at 11:37:22 3.680u 0.196s 0:04.60 84.1% 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 Sat Oct 8 2011 at 11:37:22 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 # of charge parameter records: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4669 !!! WARNING: ALA 536 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 1.661352 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): -27.24900 35.12900 ymin,ymax (A): 33.77600 98.06100 zmin,zma (A): 30.58900 89.96600 x,y,z range (A): 62.37800 64.28500 59.37700 scale (grids/A): 1.661352 object centre (A): 3.939999 65.91850 60.27750 number of atom coordinates read : 4669 total number of charged atoms : 4506 net assigned charge : -7.771962 assigned positive charge : 702.5123 centred at (gu) : 91.84435 86.75636 86.83738 assigned negative charge : -710.2883 centred at (gu) : 91.56421 86.86932 87.30341 start vw surface at 0.1200000 fill in re-entrant regions at 0.2200000 boundary points on vw surface= 101691 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35884 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 32914 mr = 73609 m= 3703 mr = 23896 m= 126 mr = 2089 m= 1 mr = 19 m= 0 mr = 0 time to grow re-entrant surface = 0.2200000 no. cavity mid-points inaccessible to solvent = 5573 time to turn everything in is 0.4900000 number of dielectric boundary points 38822 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 401 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5700000 number of grid points assigned charge 34665 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) : 0.5537839 object centre at (A) : 3.939999 65.91850 60.27750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.2102621E-04 -2.7575802E-02 midg,1,midg; midg,igrid,midg 1.6916882E-02 -1.5610063E-03 1,midg,midg; igrid,midg,midg -1.3453353E-02 1.4909502E-02 gauss-seidel spectral radius is 0.9983924 estimated iterations to convergence 198 setup time was (sec) 0.7300000 now iterating at: 11:37:23 rms-change max change #iterations 4.464048 155.7865 at 10iterations 1.959333 59.08239 at 20iterations 0.8646391 28.25415 at 30iterations 0.3800843 10.75983 at 40iterations 0.1670316 4.932999 at 50iterations 7.3595122E-02 2.143053 at 60iterations 3.2344576E-02 0.9257166 at 70iterations 1.4289957E-02 0.3799515 at 80iterations 6.3510393E-03 0.1811848 at 90iterations 2.8330872E-03 8.0502510E-02 at 100iterations 1.2886385E-03 3.8493156E-02 at 110iterations 6.0143147E-04 1.8440664E-02 at 120iterations finished qdiffx linear iterations at : 11:37:31 total time elapsed so far: 8.270000 # loops : 120 mean,max change (kT/e) : 6.0143147E-04 1.8440664E-02 energy calculations done at 8.270000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.400000 DelPhi exited at 11:37:31 8.407u 0.213s 0:09.04 95.2% 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 Sat Oct 8 2011 at 11:37:31 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 = 4669 !!! WARNING: ALA 536 has a net charge of -0.2720 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.492028 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): -27.24900 35.12900 ymin,ymax (A): 33.77600 98.06100 zmin,zma (A): 30.58900 89.96600 x,y,z range (A): 62.37800 64.28500 59.37700 scale (grids/A): 2.492028 object centre (A): 3.939999 65.91850 60.27750 number of atom coordinates read : 4669 total number of charged atoms : 4506 net assigned charge : -7.771962 assigned positive charge : 702.5123 centred at (gu) : 92.76600 85.13422 85.25583 assigned negative charge : -710.2883 centred at (gu) : 92.34615 85.30374 85.95506 start vw surface at 0.1100000 fill in re-entrant regions at 0.4500000 boundary points on vw surface= 236798 reading accessible surface arcs data from file ARCDAT no. of arc points read = 35884 grid for indexing accessible points = 1.400000 m= 114064 mr = 179178 m= 33889 mr = 93492 m= 6143 mr = 26438 m= 507 mr = 4412 m= 6 mr = 267 m= 0 mr = 0 time to grow re-entrant surface = 0.6900001 no. cavity mid-points inaccessible to solvent = 18406 time to turn everything in is 1.240000 number of dielectric boundary points 87620 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 27 iepsmp to db, and charging done at 1.340000 number of grid points assigned charge 36011 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) : 1.661352 object centre at (A) : 3.939999 65.91850 60.27750 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 4.9457915E-02 -0.3433528 midg,1,midg; midg,igrid,midg 0.3814376 -6.2096007E-03 1,midg,midg; igrid,midg,midg -0.1779416 0.1443613 gauss-seidel spectral radius is 0.9992219 estimated iterations to convergence 283 setup time was (sec) 1.490000 now iterating at: 11:37:33 rms-change max change #iterations 11.38993 298.8960 at 10iterations 6.574525 128.2235 at 20iterations 3.796381 75.95831 at 30iterations 2.173095 36.63257 at 40iterations 1.243950 23.09235 at 50iterations 0.7096637 11.79629 at 60iterations 0.4048756 6.944473 at 70iterations 0.2303832 3.994980 at 80iterations 0.1311476 2.230231 at 90iterations 7.4501880E-02 1.270773 at 100iterations 4.2321023E-02 0.7339377 at 110iterations 2.4091624E-02 0.4001980 at 120iterations 1.3688001E-02 0.2564259 at 130iterations 7.8424131E-03 0.1449509 at 140iterations 4.5071300E-03 7.5147629E-02 at 150iterations 2.6246917E-03 5.3449631E-02 at 160iterations 1.5661522E-03 2.5611877E-02 at 170iterations 9.6215494E-04 1.7867088E-02 at 180iterations finished qdiffx linear iterations at : 11:37:45 total time elapsed so far: 13.65000 # loops : 180 mean,max change (kT/e) : 9.6215494E-04 1.7867088E-02 energy calculations done at 13.65000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.78000 DelPhi exited at 11:37:46 13.780u 0.226s 0:14.27 98.1% 0+0k 0+0io 0pf+0w