Sat Oct 8 11:37:13 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 Sat Oct 8 2011 at 11:37:13 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3356 !!! WARNING: HIR 14 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: 0.6313176 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): 32.56000 86.13900 ymin,ymax (A): 25.74600 82.13600 zmin,zma (A): -3.111000 46.39700 x,y,z range (A): 53.57900 56.39000 49.50800 scale (grids/A): 0.6313176 object centre (A): 59.34950 53.94100 21.64300 number of atom coordinates read : 3356 total number of charged atoms : 3204 net assigned charge : -4.485972 assigned positive charge : 511.6403 centred at (gu) : 89.46262 89.38022 91.02820 assigned negative charge : -516.1273 centred at (gu) : 89.28440 89.49541 91.01093 start vw surface at 0.1600000 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 8711 nv = 96 ne = 84 npr = 71480 no. pairs analyzed = 71480 no. exposed pairs = 3723 no. arc points = 25494 no. surface atoms = 1276 nbur = 2080 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 472 mr = 5258 m= 4 mr = 67 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3400000 number of dielectric boundary points 3862 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2452 ## 207 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 10651 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -5.7419438E-09 -3.5986716E-09 midg,1,midg; midg,igrid,midg 1.0181063E-08 -1.6822630E-08 1,midg,midg; igrid,midg,midg -3.0588591E-08 1.4431290E-08 gauss-seidel spectral radius is 0.9870564 estimated iterations to convergence 72 setup time was (sec) 0.5500000 now iterating at: 11:37:14 rms-change max change #iterations 0.1639690 21.46424 at 10iterations 1.5765840E-02 2.166534 at 20iterations 1.5410209E-03 0.2185693 at 30iterations 1.5290616E-04 2.0029068E-02 at 40iterations 1.5384097E-05 1.9149780E-03 at 50iterations finished qdiffx linear iterations at : 11:37:16 total time elapsed so far: 2.980000 # loops : 50 mean,max change (kT/e) : 1.5384097E-05 1.9149780E-03 energy calculations done at 2.980000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.160000 DelPhi exited at 11:37:17 3.161u 0.152s 0:03.59 92.2% 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 11:37:17 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3356 !!! WARNING: HIR 14 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: 1.893953 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): 32.56000 86.13900 ymin,ymax (A): 25.74600 82.13600 zmin,zma (A): -3.111000 46.39700 x,y,z range (A): 53.57900 56.39000 49.50800 scale (grids/A): 1.893953 object centre (A): 59.34950 53.94100 21.64300 number of atom coordinates read : 3356 total number of charged atoms : 3204 net assigned charge : -4.485972 assigned positive charge : 511.6403 centred at (gu) : 88.38718 88.13986 93.08354 assigned negative charge : -516.1273 centred at (gu) : 87.85249 88.48557 93.03206 start vw surface at 0.1500000 fill in re-entrant regions at 0.2800000 boundary points on vw surface= 94261 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25494 grid for indexing accessible points = 1.400000 m= 36768 mr = 68676 m= 6045 mr = 28938 m= 352 mr = 4062 m= 3 mr = 138 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 1316 time to turn everything in is 0.6300000 number of dielectric boundary points 35615 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 143 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 25174 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) : 0.6313176 object centre at (A) : 59.34950 53.94100 21.64300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.6734818E-02 -3.4562744E-02 midg,1,midg; midg,igrid,midg 2.9295359E-02 -2.7371243E-02 1,midg,midg; igrid,midg,midg -4.9112666E-02 1.5132238E-04 gauss-seidel spectral radius is 0.9986764 estimated iterations to convergence 218 setup time was (sec) 0.9000000 now iterating at: 11:37:18 rms-change max change #iterations 4.954165 173.4368 at 10iterations 2.348647 71.85583 at 20iterations 1.116298 33.48910 at 30iterations 0.5300609 15.29399 at 40iterations 0.2505089 7.464122 at 50iterations 0.1187571 3.323878 at 60iterations 5.6532077E-02 1.506115 at 70iterations 2.6872294E-02 0.7769566 at 80iterations 1.2767829E-02 0.3539715 at 90iterations 6.0669780E-03 0.2041950 at 100iterations 2.8816629E-03 8.6017609E-02 at 110iterations 1.3674055E-03 4.0513039E-02 at 120iterations finished qdiffx linear iterations at : 11:37:24 total time elapsed so far: 6.870000 # loops : 120 mean,max change (kT/e) : 1.3674055E-03 4.0513039E-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) 7.050000 DelPhi exited at 11:37:25 7.049u 0.151s 0:07.68 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 Sat Oct 8 2011 at 11:37:25 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: 262 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3356 !!! WARNING: HIR 14 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: 2.840929 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): 32.56000 86.13900 ymin,ymax (A): 25.74600 82.13600 zmin,zma (A): -3.111000 46.39700 x,y,z range (A): 53.57900 56.39000 49.50800 scale (grids/A): 2.840929 object centre (A): 59.34950 53.94100 21.64300 number of atom coordinates read : 3356 total number of charged atoms : 3204 net assigned charge : -4.485972 assigned positive charge : 511.6403 centred at (gu) : 87.58044 87.20959 94.62502 assigned negative charge : -516.1273 centred at (gu) : 86.77879 87.72812 94.54787 start vw surface at 0.1600000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 218000 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25494 grid for indexing accessible points = 1.400000 m= 117088 mr = 165248 m= 44956 mr = 99531 m= 11251 mr = 37903 m= 1580 mr = 8776 m= 82 mr = 1089 m= 0 mr = 38 time to grow re-entrant surface = 0.9900000 no. cavity mid-points inaccessible to solvent = 4295 time to turn everything in is 1.640000 number of dielectric boundary points 80372 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.760000 number of grid points assigned charge 25628 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) : 1.893953 object centre at (A) : 59.34950 53.94100 21.64300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1967285 -0.3140421 midg,1,midg; midg,igrid,midg 0.5593486 1.8675681E-02 1,midg,midg; igrid,midg,midg -0.5368568 -0.2886495 gauss-seidel spectral radius is 0.9992739 estimated iterations to convergence 293 setup time was (sec) 1.920000 now iterating at: 11:37:27 rms-change max change #iterations 11.44507 275.2212 at 10iterations 6.706120 138.3542 at 20iterations 3.900302 71.02101 at 30iterations 2.259631 40.65821 at 40iterations 1.312531 23.96873 at 50iterations 0.7621030 12.94561 at 60iterations 0.4403861 7.462599 at 70iterations 0.2543435 4.281647 at 80iterations 0.1472850 2.812099 at 90iterations 8.4855072E-02 1.419056 at 100iterations 4.9069121E-02 0.8734816 at 110iterations 2.8386962E-02 0.4335365 at 120iterations 1.6396791E-02 0.2518158 at 130iterations 9.4784684E-03 0.1473694 at 140iterations 5.4796888E-03 8.0849648E-02 at 150iterations 3.1659936E-03 4.8412323E-02 at 160iterations 1.8312401E-03 2.9140472E-02 at 170iterations 1.0572876E-03 1.7092705E-02 at 180iterations finished qdiffx linear iterations at : 11:37:40 total time elapsed so far: 13.96000 # loops : 180 mean,max change (kT/e) : 1.0572876E-03 1.7092705E-02 energy calculations done at 13.96000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.13000 DelPhi exited at 11:37:40 14.130u 0.185s 0:15.77 90.7% 0+0k 0+0io 0pf+0w