Sun Oct 9 13:43:15 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+sph2.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 = amb2.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 13:43:15 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2383 !!! WARNING: GLM 182 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.7014502 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): -6.728000 44.02400 ymin,ymax (A): -14.13400 35.83500 zmin,zma (A): 1.668000 44.52100 x,y,z range (A): 50.75200 49.96900 42.85300 scale (grids/A): 0.7014502 object centre (A): 18.64800 10.85050 23.09450 number of atom coordinates read : 2383 total number of charged atoms : 2239 net assigned charge : 4.406011 assigned positive charge : 364.8192 centred at (gu) : 89.71006 91.40727 90.89450 assigned negative charge : -360.4136 centred at (gu) : 89.70254 91.56023 91.02265 start vw surface at 0.1400000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 7970 nv = 96 ne = 84 npr = 47835 no. pairs analyzed = 47835 no. exposed pairs = 2986 no. arc points = 21176 no. surface atoms = 1011 nbur = 1372 mkacc time = 9.9999994E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 510 mr = 4432 m= 2 mr = 99 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 0.2800000 number of dielectric boundary points 3951 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1898 ## 172 charges are in solution ## iepsmp to db, and charging done at 0.3900000 number of grid points assigned charge 8882 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.1429171E-08 -3.6947164E-08 midg,1,midg; midg,igrid,midg 8.2769418E-08 -5.8201408E-08 1,midg,midg; igrid,midg,midg 3.2072389E-08 3.5809506E-08 gauss-seidel spectral radius is 0.9894406 estimated iterations to convergence 79 setup time was (sec) 0.5000000 now iterating at: 13:43:16 rms-change max change #iterations 0.2090541 25.02488 at 10iterations 2.5938209E-02 3.931668 at 20iterations 3.8029579E-03 0.6214066 at 30iterations 8.7538804E-04 0.1358452 at 40iterations 2.9132003E-04 4.7981262E-02 at 50iterations finished qdiffx linear iterations at : 13:43:18 total time elapsed so far: 2.910000 # loops : 50 mean,max change (kT/e) : 2.9132003E-04 4.7981262E-02 energy calculations done at 2.910000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.080000 DelPhi exited at 13:43:19 3.083u 0.133s 0:03.52 91.1% 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 Sun Oct 9 2011 at 13:43:19 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2383 !!! WARNING: GLM 182 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.104351 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): -6.728000 44.02400 ymin,ymax (A): -14.13400 35.83500 zmin,zma (A): 1.668000 44.52100 x,y,z range (A): 50.75200 49.96900 42.85300 scale (grids/A): 2.104351 object centre (A): 18.64800 10.85050 23.09450 number of atom coordinates read : 2383 total number of charged atoms : 2239 net assigned charge : 4.406011 assigned positive charge : 364.8192 centred at (gu) : 89.12986 94.22160 92.68283 assigned negative charge : -360.4136 centred at (gu) : 89.10736 94.68046 93.06783 start vw surface at 0.1400000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 83886 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21176 grid for indexing accessible points = 1.400000 m= 32270 mr = 58080 m= 6016 mr = 24007 m= 609 mr = 4045 m= 12 mr = 318 m= 0 mr = 0 time to grow re-entrant surface = 0.2900000 no. cavity mid-points inaccessible to solvent = 418 time to turn everything in is 0.5900000 number of dielectric boundary points 36343 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 98 iepsmp to db, and charging done at 0.7100000 number of grid points assigned charge 17789 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) : 0.7014502 object centre at (A) : 18.64800 10.85050 23.09450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 5.9931871E-02 -1.3141468E-04 midg,1,midg; midg,igrid,midg 1.7147517E-02 -4.8339937E-02 1,midg,midg; igrid,midg,midg 5.4691173E-02 1.4114821E-03 gauss-seidel spectral radius is 0.9988511 estimated iterations to convergence 233 setup time was (sec) 0.8500000 now iterating at: 13:43:20 rms-change max change #iterations 4.969800 254.1550 at 10iterations 2.463340 83.73278 at 20iterations 1.229496 35.24889 at 30iterations 0.6134941 18.82182 at 40iterations 0.3069803 8.833527 at 50iterations 0.1529939 4.654307 at 60iterations 7.6297000E-02 2.239487 at 70iterations 3.8323924E-02 1.135614 at 80iterations 1.9255511E-02 0.5468407 at 90iterations 9.7917970E-03 0.3377295 at 100iterations 5.0436566E-03 0.1428108 at 110iterations 2.6932659E-03 8.3057404E-02 at 120iterations finished qdiffx linear iterations at : 13:43:26 total time elapsed so far: 6.870000 # loops : 120 mean,max change (kT/e) : 2.6932659E-03 8.3057404E-02 energy calculations done at 6.870000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.060000 DelPhi exited at 13:43:26 7.058u 0.155s 0:07.56 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 Sun Oct 9 2011 at 13:43:26 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: 302 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2383 !!! WARNING: GLM 182 has a net charge of -0.0940 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 3.156526 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): -6.728000 44.02400 ymin,ymax (A): -14.13400 35.83500 zmin,zma (A): 1.668000 44.52100 x,y,z range (A): 50.75200 49.96900 42.85300 scale (grids/A): 3.156526 object centre (A): 18.64800 10.85050 23.09450 number of atom coordinates read : 2383 total number of charged atoms : 2239 net assigned charge : 4.406011 assigned positive charge : 364.8192 centred at (gu) : 88.69465 96.33212 94.02423 assigned negative charge : -360.4136 centred at (gu) : 88.66103 97.02068 94.60161 start vw surface at 0.1400000 fill in re-entrant regions at 0.8400000 boundary points on vw surface= 193366 reading accessible surface arcs data from file ARCDAT no. of arc points read = 21176 grid for indexing accessible points = 1.400000 m= 101546 mr = 140166 m= 40132 mr = 83603 m= 11342 mr = 32620 m= 2388 mr = 8777 m= 255 mr = 1794 m= 2 mr = 166 m= 0 mr = 0 time to grow re-entrant surface = 0.9000000 no. cavity mid-points inaccessible to solvent = 1297 time to turn everything in is 1.840000 number of dielectric boundary points 81905 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.960000 number of grid points assigned charge 17912 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) : 2.104351 object centre at (A) : 18.64800 10.85050 23.09450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.5287282 -9.0555295E-02 midg,1,midg; midg,igrid,midg 0.3275921 -0.5018116 1,midg,midg; igrid,midg,midg 0.5862430 -0.3529131 gauss-seidel spectral radius is 0.9993051 estimated iterations to convergence 299 setup time was (sec) 2.110000 now iterating at: 13:43:29 rms-change max change #iterations 11.11290 501.8611 at 10iterations 6.628554 127.2089 at 20iterations 3.924146 74.72742 at 30iterations 2.329066 42.83258 at 40iterations 1.378226 25.20875 at 50iterations 0.8130615 14.58091 at 60iterations 0.4787759 7.982617 at 70iterations 0.2821554 4.710061 at 80iterations 0.1659514 2.984029 at 90iterations 9.7721770E-02 1.512704 at 100iterations 5.7498001E-02 0.9445090 at 110iterations 3.4115572E-02 0.6148663 at 120iterations 2.0353943E-02 0.3497009 at 130iterations 1.2396893E-02 0.2346745 at 140iterations 7.7821813E-03 0.1568146 at 150iterations 5.1207617E-03 0.1239624 at 160iterations 3.5747755E-03 7.8346252E-02 at 170iterations 2.6679977E-03 5.7476044E-02 at 180iterations finished qdiffx linear iterations at : 13:43:38 total time elapsed so far: 11.61000 # loops : 180 mean,max change (kT/e) : 2.6679977E-03 5.7476044E-02 energy calculations done at 11.61000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.78000 DelPhi exited at 13:43:39 11.784u 0.183s 0:12.34 96.9% 0+0k 0+0io 0pf+0w