Mon Oct 10 19:33:39 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 Mon Oct 10 2011 at 19:33:40 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3221 !!! WARNING: HIT 103 has a net charge of 0.5140 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: 0.5633268 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): -31.25800 31.93800 ymin,ymax (A): -23.21300 25.33900 zmin,zma (A): -4.205000 54.26600 x,y,z range (A): 63.19600 48.55200 58.47100 scale (grids/A): 0.5633268 object centre (A): 0.3400002 1.062999 25.03050 number of atom coordinates read : 3221 total number of charged atoms : 3081 net assigned charge : 2.514020 assigned positive charge : 490.6064 centred at (gu) : 91.00768 89.80156 91.71456 assigned negative charge : -488.0938 centred at (gu) : 91.01207 89.67606 91.65325 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 6822 nv = 96 ne = 84 npr = 62116 no. pairs analyzed = 62116 no. exposed pairs = 4459 no. arc points = 31907 no. surface atoms = 1498 nbur = 1723 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= 323 mr = 3318 m= 0 mr = 14 time to grow re-entrant surface = 0.2000000 no. cavity mid-points inaccessible to solvent = 5 time to turn everything in is 0.3500000 number of dielectric boundary points 3813 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3236 ## 414 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 8806 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.5955830E-10 1.7022156E-09 midg,1,midg; midg,igrid,midg -1.5184396E-09 1.8819448E-09 1,midg,midg; igrid,midg,midg 2.7723618E-10 2.9138569E-10 gauss-seidel spectral radius is 0.9837753 estimated iterations to convergence 65 setup time was (sec) 0.6600000 now iterating at: 19:33:41 rms-change max change #iterations 9.0101473E-02 17.34776 at 10iterations 6.5704864E-03 1.051300 at 20iterations 4.9213960E-04 7.6156616E-02 at 30iterations 4.6607278E-05 6.7005157E-03 at 40iterations 7.0183564E-06 1.2197495E-03 at 50iterations finished qdiffx linear iterations at : 19:33:45 total time elapsed so far: 4.690000 # loops : 50 mean,max change (kT/e) : 7.0183564E-06 1.2197495E-03 energy calculations done at 4.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.860000 DelPhi exited at 19:33:45 4.862u 0.373s 0:05.94 88.0% 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 19:33:46 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3221 !!! WARNING: HIT 103 has a net charge of 0.5140 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: 1.689980 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): -31.25800 31.93800 ymin,ymax (A): -23.21300 25.33900 zmin,zma (A): -4.205000 54.26600 x,y,z range (A): 63.19600 48.55200 58.47100 scale (grids/A): 1.689980 object centre (A): 0.3400002 1.062999 25.03050 number of atom coordinates read : 3221 total number of charged atoms : 3081 net assigned charge : 2.514020 assigned positive charge : 490.6064 centred at (gu) : 93.02176 89.40375 95.14291 assigned negative charge : -488.0938 centred at (gu) : 93.03602 89.02782 94.95950 start vw surface at 0.1300000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 74920 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31907 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 23492 mr = 48676 m= 2719 mr = 15622 m= 103 mr = 1267 m= 0 mr = 7 time to grow re-entrant surface = 0.3200000 no. cavity mid-points inaccessible to solvent = 1247 time to turn everything in is 0.6100000 number of dielectric boundary points 35662 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 328 ## 3 charges are in solution ## iepsmp to db, and charging done at 0.7300000 number of grid points assigned charge 23839 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) : 0.5633268 object centre at (A) : 0.3400002 1.062999 25.03050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.9633669E-02 1.9525651E-02 midg,1,midg; midg,igrid,midg -1.9736750E-02 1.0005799E-02 1,midg,midg; igrid,midg,midg 1.9451900E-03 4.6486021E-03 gauss-seidel spectral radius is 0.9983567 estimated iterations to convergence 196 setup time was (sec) 0.9300000 now iterating at: 19:33:47 rms-change max change #iterations 3.799207 171.9495 at 10iterations 1.635939 54.58387 at 20iterations 0.7082284 23.93687 at 30iterations 0.3073973 11.29391 at 40iterations 0.1329808 4.743919 at 50iterations 5.7834778E-02 1.923397 at 60iterations 2.5089094E-02 0.8938942 at 70iterations 1.0903290E-02 0.3965893 at 80iterations 4.7372244E-03 0.1753616 at 90iterations 2.0566201E-03 7.6150894E-02 at 100iterations 8.9553691E-04 3.2619476E-02 at 110iterations 3.9176131E-04 1.3305664E-02 at 120iterations finished qdiffx linear iterations at : 19:33:58 total time elapsed so far: 11.68000 # loops : 120 mean,max change (kT/e) : 3.9176131E-04 1.3305664E-02 energy calculations done at 11.68000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.86000 DelPhi exited at 19:33:58 11.867u 0.426s 0:12.90 95.1% 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 Mon Oct 10 2011 at 19:33:58 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: 316 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3221 !!! WARNING: HIT 103 has a net charge of 0.5140 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: 2.534971 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): -31.25800 31.93800 ymin,ymax (A): -23.21300 25.33900 zmin,zma (A): -4.205000 54.26600 x,y,z range (A): 63.19600 48.55200 58.47100 scale (grids/A): 2.534971 object centre (A): 0.3400002 1.062999 25.03050 number of atom coordinates read : 3221 total number of charged atoms : 3081 net assigned charge : 2.514020 assigned positive charge : 490.6064 centred at (gu) : 94.53251 89.10545 97.71404 assigned negative charge : -488.0938 centred at (gu) : 94.55396 88.54167 97.43926 start vw surface at 0.1300000 fill in re-entrant regions at 0.4800000 boundary points on vw surface= 173777 reading accessible surface arcs data from file ARCDAT no. of arc points read = 31907 grid for indexing accessible points = 1.400000 m= 79624 mr = 119613 m= 23862 mr = 61403 m= 4290 mr = 17457 m= 434 mr = 2691 m= 12 mr = 209 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.9300000 no. cavity mid-points inaccessible to solvent = 4162 time to turn everything in is 1.520000 number of dielectric boundary points 80627 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.650000 number of grid points assigned charge 24636 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) : 1.689980 object centre at (A) : 0.3400002 1.062999 25.03050 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4323611 0.2335118 midg,1,midg; midg,igrid,midg -0.2393968 0.1589268 1,midg,midg; igrid,midg,midg 0.4318821 0.1347603 gauss-seidel spectral radius is 0.9992121 estimated iterations to convergence 281 setup time was (sec) 1.850000 now iterating at: 19:34:01 rms-change max change #iterations 9.763332 324.9010 at 10iterations 5.618869 164.3678 at 20iterations 3.219931 70.77969 at 30iterations 1.835696 41.96840 at 40iterations 1.042989 21.98959 at 50iterations 0.5931287 14.34095 at 60iterations 0.3355255 6.182554 at 70iterations 0.1904567 4.207923 at 80iterations 0.1075454 2.392478 at 90iterations 6.0675312E-02 1.211252 at 100iterations 3.4280930E-02 0.6783619 at 110iterations 1.9345151E-02 0.3995438 at 120iterations 1.0911466E-02 0.2064743 at 130iterations 6.1700055E-03 0.1184464 at 140iterations 3.4703531E-03 6.7594528E-02 at 150iterations 1.9606724E-03 3.7403107E-02 at 160iterations 1.1059918E-03 2.1070480E-02 at 170iterations 6.2279805E-04 1.1909962E-02 at 180iterations finished qdiffx linear iterations at : 19:34:18 total time elapsed so far: 18.82000 # loops : 180 mean,max change (kT/e) : 6.2279805E-04 1.1909962E-02 energy calculations done at 18.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 19.00000 DelPhi exited at 19:34:18 19.001u 0.464s 0:19.79 98.3% 0+0k 0+0io 0pf+0w