Tue Oct 11 06:00:21 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 Tue Oct 11 2011 at 06:00:21 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2061 !!! WARNING: GLM 175 has a net charge of -0.0940 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.7608789 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): -18.02600 28.76200 ymin,ymax (A): -11.74500 30.71900 zmin,zma (A): -8.487000 38.07900 x,y,z range (A): 46.78800 42.46400 46.56600 scale (grids/A): 0.7608789 object centre (A): 5.368000 9.487000 14.79600 number of atom coordinates read : 2061 total number of charged atoms : 1923 net assigned charge : 6.837009 assigned positive charge : 312.6271 centred at (gu) : 90.57658 89.85161 90.98640 assigned negative charge : -305.7902 centred at (gu) : 90.43369 89.78813 90.85690 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 8320 nv = 96 ne = 84 npr = 41344 no. pairs analyzed = 41344 no. exposed pairs = 2518 no. arc points = 17237 no. surface atoms = 854 nbur = 1207 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 624 mr = 4944 m= 6 mr = 136 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 6 time to turn everything in is 0.1700000 number of dielectric boundary points 3870 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1429 ## 114 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 8558 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.1598161E-09 4.4517824E-07 midg,1,midg; midg,igrid,midg 9.2483511E-08 2.6939952E-07 1,midg,midg; igrid,midg,midg -2.4505493E-08 4.3435551E-07 gauss-seidel spectral radius is 0.9909848 estimated iterations to convergence 85 setup time was (sec) 0.3500000 now iterating at: 06:00:22 rms-change max change #iterations 0.2712182 39.77019 at 10iterations 3.9245941E-02 4.987604 at 20iterations 5.8622649E-03 0.7919388 at 30iterations 9.8789867E-04 0.1149673 at 40iterations 2.3829755E-04 2.7746201E-02 at 50iterations finished qdiffx linear iterations at : 06:00:24 total time elapsed so far: 3.190000 # loops : 50 mean,max change (kT/e) : 2.3829755E-04 2.7746201E-02 energy calculations done at 3.190000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.310000 DelPhi exited at 06:00:25 3.314u 0.183s 0:03.78 92.3% 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 Tue Oct 11 2011 at 06:00:25 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2061 !!! WARNING: GLM 175 has a net charge of -0.0940 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.282637 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): -18.02600 28.76200 ymin,ymax (A): -11.74500 30.71900 zmin,zma (A): -8.487000 38.07900 x,y,z range (A): 46.78800 42.46400 46.56600 scale (grids/A): 2.282637 object centre (A): 5.368000 9.487000 14.79600 number of atom coordinates read : 2061 total number of charged atoms : 1923 net assigned charge : 6.837009 assigned positive charge : 312.6271 centred at (gu) : 91.72993 89.55505 92.95916 assigned negative charge : -305.7902 centred at (gu) : 91.30106 89.36450 92.57086 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 86782 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17237 grid for indexing accessible points = 1.400000 m= 38069 mr = 62307 m= 8668 mr = 29698 m= 1030 mr = 6120 m= 48 mr = 605 m= 0 mr = 7 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 201 time to turn everything in is 0.4400000 number of dielectric boundary points 35860 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 37 iepsmp to db, and charging done at 0.5200000 number of grid points assigned charge 15334 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) : 0.7608789 object centre at (A) : 5.368000 9.487000 14.79600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.8407139E-02 5.6065027E-02 midg,1,midg; midg,igrid,midg 3.6615655E-02 3.1902451E-02 1,midg,midg; igrid,midg,midg 4.2511672E-02 0.1210689 gauss-seidel spectral radius is 0.9989642 estimated iterations to convergence 246 setup time was (sec) 0.6600000 now iterating at: 06:00:26 rms-change max change #iterations 5.226169 222.7511 at 10iterations 2.714333 97.97832 at 20iterations 1.397451 46.74387 at 30iterations 0.7239529 19.07868 at 40iterations 0.3744977 9.699979 at 50iterations 0.1933376 5.857796 at 60iterations 0.1002502 2.526363 at 70iterations 5.1975351E-02 1.584732 at 80iterations 2.7057000E-02 0.6934252 at 90iterations 1.4137272E-02 0.4170227 at 100iterations 7.4305809E-03 0.1998549 at 110iterations 3.9512441E-03 0.1077919 at 120iterations finished qdiffx linear iterations at : 06:00:33 total time elapsed so far: 7.700000 # loops : 120 mean,max change (kT/e) : 3.9512441E-03 0.1077919 energy calculations done at 7.700000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.830000 DelPhi exited at 06:00:33 7.834u 0.197s 0:08.56 93.6% 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 Tue Oct 11 2011 at 06:00:33 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: 294 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2061 !!! WARNING: GLM 175 has a net charge of -0.0940 !!! WARNING: SEP 190 has a net charge of -0.4750 !!! WARNING: GLM 192 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= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.423955 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): -18.02600 28.76200 ymin,ymax (A): -11.74500 30.71900 zmin,zma (A): -8.487000 38.07900 x,y,z range (A): 46.78800 42.46400 46.56600 scale (grids/A): 3.423955 object centre (A): 5.368000 9.487000 14.79600 number of atom coordinates read : 2061 total number of charged atoms : 1923 net assigned charge : 6.837009 assigned positive charge : 312.6271 centred at (gu) : 92.59492 89.33267 94.43871 assigned negative charge : -305.7902 centred at (gu) : 91.95161 89.04678 93.85629 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 199168 reading accessible surface arcs data from file ARCDAT no. of arc points read = 17237 grid for indexing accessible points = 1.400000 m= 114378 mr = 149026 m= 51822 mr = 96516 m= 17113 mr = 43683 m= 4134 mr = 13720 m= 673 mr = 3187 m= 55 mr = 469 m= 5 mr = 23 m= 0 mr = 0 time to grow re-entrant surface = 0.7500000 no. cavity mid-points inaccessible to solvent = 735 time to turn everything in is 1.410000 number of dielectric boundary points 80724 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.500000 number of grid points assigned charge 15384 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) : 2.282637 object centre at (A) : 5.368000 9.487000 14.79600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.6318209 0.4996593 midg,1,midg; midg,igrid,midg 0.2936809 0.1243158 1,midg,midg; igrid,midg,midg 0.2245528 0.7973083 gauss-seidel spectral radius is 0.9993317 estimated iterations to convergence 305 setup time was (sec) 1.650000 now iterating at: 06:00:35 rms-change max change #iterations 11.26660 260.3967 at 10iterations 6.808929 150.6919 at 20iterations 4.084659 80.57595 at 30iterations 2.443888 44.18041 at 40iterations 1.459253 31.35695 at 50iterations 0.8737907 15.10966 at 60iterations 0.5197782 8.657434 at 70iterations 0.3095913 5.162045 at 80iterations 0.1846170 3.457775 at 90iterations 0.1099058 1.792257 at 100iterations 6.5418139E-02 1.156448 at 110iterations 3.9247107E-02 0.6870422 at 120iterations 2.3654908E-02 0.3947306 at 130iterations 1.4506423E-02 0.2560043 at 140iterations 9.1459956E-03 0.1548996 at 150iterations 6.0109673E-03 0.1056786 at 160iterations 4.1659954E-03 7.0808411E-02 at 170iterations 3.0646215E-03 5.7659149E-02 at 180iterations finished qdiffx linear iterations at : 06:00:47 total time elapsed so far: 12.98000 # loops : 180 mean,max change (kT/e) : 3.0646215E-03 5.7659149E-02 energy calculations done at 12.98000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.11000 DelPhi exited at 06:00:47 13.110u 0.205s 0:13.69 97.2% 0+0k 0+0io 0pf+0w