Tue Oct 11 07:58:32 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 07:58:32 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2314 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6696386 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): -58.19000 -5.027000 ymin,ymax (A): 65.86200 108.1660 zmin,zma (A): -24.96600 19.45300 x,y,z range (A): 53.16300 42.30400 44.41900 scale (grids/A): 0.6696386 object centre (A): -31.60850 87.01400 -2.756500 number of atom coordinates read : 2314 total number of charged atoms : 2188 net assigned charge : 4.025008 assigned positive charge : 348.2755 centred at (gu) : 91.54893 90.32491 90.62718 assigned negative charge : -344.2509 centred at (gu) : 91.67486 90.50494 90.54124 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 6896 nv = 96 ne = 84 npr = 47140 no. pairs analyzed = 47140 no. exposed pairs = 2795 no. arc points = 19975 no. surface atoms = 943 nbur = 1371 mkacc time = 7.9999998E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 363 mr = 3841 m= 3 mr = 46 m= 0 mr = 0 time to grow re-entrant surface = 9.0000004E-02 no. cavity mid-points inaccessible to solvent = 126 time to turn everything in is 0.1700000 number of dielectric boundary points 3375 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1870 ## 182 charges are in solution ## iepsmp to db, and charging done at 0.2300000 number of grid points assigned charge 8113 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.8136184E-09 3.7282131E-08 midg,1,midg; midg,igrid,midg 4.9741317E-08 -2.9151373E-08 1,midg,midg; igrid,midg,midg 3.0260015E-08 -2.0767361E-08 gauss-seidel spectral radius is 0.9884110 estimated iterations to convergence 76 setup time was (sec) 0.3500000 now iterating at: 07:58:33 rms-change max change #iterations 0.1677245 25.73176 at 10iterations 1.8384246E-02 2.412136 at 20iterations 2.0386567E-03 0.3002493 at 30iterations 2.1894449E-04 3.2876730E-02 at 40iterations 2.3807184E-05 3.3493042E-03 at 50iterations finished qdiffx linear iterations at : 07:58:36 total time elapsed so far: 3.500000 # loops : 50 mean,max change (kT/e) : 2.3807184E-05 3.3493042E-03 energy calculations done at 3.500000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.630000 DelPhi exited at 07:58:37 3.638u 0.183s 0:04.34 87.7% 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 07:58:37 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2314 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.008916 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): -58.19000 -5.027000 ymin,ymax (A): 65.86200 108.1660 zmin,zma (A): -24.96600 19.45300 x,y,z range (A): 53.16300 42.30400 44.41900 scale (grids/A): 2.008916 object centre (A): -31.60850 87.01400 -2.756500 number of atom coordinates read : 2314 total number of charged atoms : 2188 net assigned charge : 4.025008 assigned positive charge : 348.2755 centred at (gu) : 94.64651 90.97433 91.88122 assigned negative charge : -344.2509 centred at (gu) : 95.02459 91.51465 91.62373 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 74007 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19975 grid for indexing accessible points = 1.400000 m= 27598 mr = 51627 m= 4656 mr = 20656 m= 324 mr = 3047 m= 7 mr = 122 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 1312 time to turn everything in is 0.3600000 number of dielectric boundary points 31140 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 112 iepsmp to db, and charging done at 0.4300000 number of grid points assigned charge 17311 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) : 0.6696386 object centre at (A) : -31.60850 87.01400 -2.756500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.1935901E-02 3.0428600E-02 midg,1,midg; midg,igrid,midg 2.4917787E-02 -2.7648494E-02 1,midg,midg; igrid,midg,midg 5.1452797E-02 2.8151939E-02 gauss-seidel spectral radius is 0.9987370 estimated iterations to convergence 223 setup time was (sec) 0.5600000 now iterating at: 07:58:38 rms-change max change #iterations 4.398798 207.0828 at 10iterations 2.114799 84.35101 at 20iterations 1.018975 35.74231 at 30iterations 0.4916813 15.31173 at 40iterations 0.2380595 7.629898 at 50iterations 0.1144764 4.125345 at 60iterations 5.5226699E-02 1.755979 at 70iterations 2.6678652E-02 0.8952093 at 80iterations 1.2877910E-02 0.3963810 at 90iterations 6.1961627E-03 0.2036085 at 100iterations 2.9967923E-03 0.1005640 at 110iterations 1.4450279E-03 4.4647217E-02 at 120iterations finished qdiffx linear iterations at : 07:58:45 total time elapsed so far: 7.520000 # loops : 120 mean,max change (kT/e) : 1.4450279E-03 4.4647217E-02 energy calculations done at 7.520000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.650000 DelPhi exited at 07:58:45 7.654u 0.205s 0:08.15 96.3% 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 07:58:45 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: 277 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2314 !!! WARNING: SEP 190 has a net charge of -0.4750 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 3.9999999E-02 grid size : 179 scale,in grids/A, set to be: 3.013374 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): -58.19000 -5.027000 ymin,ymax (A): 65.86200 108.1660 zmin,zma (A): -24.96600 19.45300 x,y,z range (A): 53.16300 42.30400 44.41900 scale (grids/A): 3.013374 object centre (A): -31.60850 87.01400 -2.756500 number of atom coordinates read : 2314 total number of charged atoms : 2188 net assigned charge : 4.025008 assigned positive charge : 348.2755 centred at (gu) : 96.96967 91.46149 92.82177 assigned negative charge : -344.2509 centred at (gu) : 97.53680 92.27196 92.43546 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.3300000 boundary points on vw surface= 170615 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19975 grid for indexing accessible points = 1.400000 m= 88176 mr = 124447 m= 33054 mr = 72860 m= 8599 mr = 26884 m= 1376 mr = 6624 m= 104 mr = 916 m= 7 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.5400000 no. cavity mid-points inaccessible to solvent = 4561 time to turn everything in is 0.9600000 number of dielectric boundary points 70134 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.040000 number of grid points assigned charge 17502 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) : 2.008916 object centre at (A) : -31.60850 87.01400 -2.756500 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2120628 0.3156284 midg,1,midg; midg,igrid,midg 0.1500096 -0.3218575 1,midg,midg; igrid,midg,midg 0.5902319 0.2960740 gauss-seidel spectral radius is 0.9992765 estimated iterations to convergence 293 setup time was (sec) 1.190000 now iterating at: 07:58:46 rms-change max change #iterations 10.10727 550.1570 at 10iterations 5.905106 151.2283 at 20iterations 3.447264 69.10502 at 30iterations 2.009947 39.99026 at 40iterations 1.167605 22.61152 at 50iterations 0.6787559 12.60434 at 60iterations 0.3942300 7.649426 at 70iterations 0.2286322 4.061852 at 80iterations 0.1324659 2.639191 at 90iterations 7.6487146E-02 1.397537 at 100iterations 4.4226795E-02 0.8216476 at 110iterations 2.5680173E-02 0.4513008 at 120iterations 1.4844441E-02 0.2601666 at 130iterations 8.6002536E-03 0.1537704 at 140iterations 4.9647316E-03 8.6776733E-02 at 150iterations 2.8743851E-03 5.0568581E-02 at 160iterations 1.6679438E-03 3.0080795E-02 at 170iterations 9.6609566E-04 1.8068314E-02 at 180iterations finished qdiffx linear iterations at : 07:58:57 total time elapsed so far: 12.28000 # loops : 180 mean,max change (kT/e) : 9.6609566E-04 1.8068314E-02 energy calculations done at 12.28000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.40000 DelPhi exited at 07:58:58 12.404u 0.194s 0:13.05 96.4% 0+0k 0+0io 0pf+0w