Sat Oct 8 20:04:37 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+sph.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 = amb.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 20:04:37 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2619 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 657 has a net charge of 1.4000 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: 0.6168882 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): -32.16200 17.54800 ymin,ymax (A): -24.45600 23.14900 zmin,zma (A): -12.39600 45.31300 x,y,z range (A): 49.71000 47.60500 57.70900 scale (grids/A): 0.6168882 object centre (A): -7.306999 -0.6534996 16.45850 number of atom coordinates read : 2619 total number of charged atoms : 2475 net assigned charge : 3.500007 assigned positive charge : 395.4500 centred at (gu) : 88.74904 89.31557 89.50378 assigned negative charge : -391.9505 centred at (gu) : 88.64879 89.36944 89.41359 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1000000 boundary points on vw surface= 6424 nv = 96 ne = 84 npr = 54973 no. pairs analyzed = 54973 no. exposed pairs = 3078 no. arc points = 22122 no. surface atoms = 1030 nbur = 1589 mkacc time = 8.9999996E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 294 mr = 3527 m= 2 mr = 24 m= 0 mr = 0 time to grow re-entrant surface = 9.9999987E-02 no. cavity mid-points inaccessible to solvent = 59 time to turn everything in is 0.2100000 number of dielectric boundary points 3169 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2247 ## 251 charges are in solution ## iepsmp to db, and charging done at 0.2800000 number of grid points assigned charge 8090 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -3.2828211E-09 7.2711872E-09 midg,1,midg; midg,igrid,midg 6.8983290E-09 -5.4847654E-10 1,midg,midg; igrid,midg,midg -4.7661310E-09 6.6163701E-09 gauss-seidel spectral radius is 0.9863896 estimated iterations to convergence 70 setup time was (sec) 0.4000000 now iterating at: 20:04:38 rms-change max change #iterations 0.1238506 18.40104 at 10iterations 1.1221223E-02 1.655666 at 20iterations 1.0141617E-03 0.1659470 at 30iterations 9.3159710E-05 1.3118505E-02 at 40iterations 8.4158764E-06 1.2931824E-03 at 50iterations finished qdiffx linear iterations at : 20:04:40 total time elapsed so far: 3.300000 # loops : 50 mean,max change (kT/e) : 8.4158764E-06 1.2931824E-03 energy calculations done at 3.300000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.430000 DelPhi exited at 20:04:41 3.435u 0.184s 0:03.91 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 Sat Oct 8 2011 at 20:04:41 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2619 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 657 has a net charge of 1.4000 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: 1.850664 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): -32.16200 17.54800 ymin,ymax (A): -24.45600 23.14900 zmin,zma (A): -12.39600 45.31300 x,y,z range (A): 49.71000 47.60500 57.70900 scale (grids/A): 1.850664 object centre (A): -7.306999 -0.6534996 16.45850 number of atom coordinates read : 2619 total number of charged atoms : 2475 net assigned charge : 3.500007 assigned positive charge : 395.4500 centred at (gu) : 86.24689 87.94611 88.51075 assigned negative charge : -391.9505 centred at (gu) : 85.94613 88.10807 88.24062 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.1600000 boundary points on vw surface= 70387 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22122 grid for indexing accessible points = 1.400000 m= 23266 mr = 48939 m= 3072 mr = 16832 m= 138 mr = 1832 m= 3 mr = 29 m= 0 mr = 0 time to grow re-entrant surface = 0.1500000 no. cavity mid-points inaccessible to solvent = 5689 time to turn everything in is 0.3400000 number of dielectric boundary points 29234 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 172 iepsmp to db, and charging done at 0.4200000 number of grid points assigned charge 19405 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) : 0.6168882 object centre at (A) : -7.306999 -0.6534996 16.45850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.1824175E-02 1.9482715E-02 midg,1,midg; midg,igrid,midg 1.0634033E-02 -2.1559589E-03 1,midg,midg; igrid,midg,midg -3.3194278E-03 2.7041404E-02 gauss-seidel spectral radius is 0.9985566 estimated iterations to convergence 209 setup time was (sec) 0.5600000 now iterating at: 20:04:42 rms-change max change #iterations 4.032553 168.9083 at 10iterations 1.847211 60.92599 at 20iterations 0.8469382 30.37922 at 30iterations 0.3886809 13.55975 at 40iterations 0.1779895 5.716856 at 50iterations 8.1654005E-02 2.680634 at 60iterations 3.7420917E-02 1.169441 at 70iterations 1.7124465E-02 0.5625248 at 80iterations 7.8559807E-03 0.2515874 at 90iterations 3.6128955E-03 0.1177387 at 100iterations 1.6583860E-03 5.4217339E-02 at 110iterations 7.5785338E-04 2.4407566E-02 at 120iterations finished qdiffx linear iterations at : 20:04:49 total time elapsed so far: 7.690000 # loops : 120 mean,max change (kT/e) : 7.5785338E-04 2.4407566E-02 energy calculations done at 7.690000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.830000 DelPhi exited at 20:04:49 7.836u 0.199s 0:08.30 96.6% 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 20:04:49 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: 257 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2619 !!! WARNING: HIZ 94 has a net charge of 0.2000 !!! WARNING: HIZ 96 has a net charge of 0.2000 !!! WARNING: HIY 119 has a net charge of 0.2000 !!! WARNING: ZN6 657 has a net charge of 1.4000 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: 2.775997 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): -32.16200 17.54800 ymin,ymax (A): -24.45600 23.14900 zmin,zma (A): -12.39600 45.31300 x,y,z range (A): 49.71000 47.60500 57.70900 scale (grids/A): 2.775997 object centre (A): -7.306999 -0.6534996 16.45850 number of atom coordinates read : 2619 total number of charged atoms : 2475 net assigned charge : 3.500007 assigned positive charge : 395.4500 centred at (gu) : 84.37009 86.91913 87.76602 assigned negative charge : -391.9505 centred at (gu) : 83.91908 87.16206 87.36074 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.3100000 boundary points on vw surface= 163146 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22122 grid for indexing accessible points = 1.400000 m= 78139 mr = 118728 m= 25236 mr = 63607 m= 5404 mr = 19950 m= 637 mr = 3908 m= 26 mr = 364 m= 0 mr = 9 time to grow re-entrant surface = 0.4800000 no. cavity mid-points inaccessible to solvent = 19473 time to turn everything in is 0.8700000 number of dielectric boundary points 66022 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 0.9600000 number of grid points assigned charge 19794 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) : 1.850664 object centre at (A) : -7.306999 -0.6534996 16.45850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.5776932E-02 0.2610157 midg,1,midg; midg,igrid,midg 0.1037696 -3.8410779E-02 1,midg,midg; igrid,midg,midg -2.0422341E-02 0.3787820 gauss-seidel spectral radius is 0.9992321 estimated iterations to convergence 285 setup time was (sec) 1.100000 now iterating at: 20:04:51 rms-change max change #iterations 9.461238 272.6856 at 10iterations 5.418724 120.0350 at 20iterations 3.089205 61.70411 at 30iterations 1.761418 42.72778 at 40iterations 1.002009 23.18243 at 50iterations 0.5711148 10.36990 at 60iterations 0.3241882 6.040427 at 70iterations 0.1843914 3.915474 at 80iterations 0.1044590 1.962865 at 90iterations 5.9475951E-02 1.168478 at 100iterations 3.3764452E-02 0.6561909 at 110iterations 1.9221731E-02 0.3728571 at 120iterations 1.0910943E-02 0.2133522 at 130iterations 6.1938753E-03 0.1212234 at 140iterations 3.5102696E-03 6.4813614E-02 at 150iterations 1.9975100E-03 3.6002159E-02 at 160iterations 1.1324892E-03 2.2098541E-02 at 170iterations 6.4348336E-04 1.2912750E-02 at 180iterations finished qdiffx linear iterations at : 20:05:02 total time elapsed so far: 12.43000 # loops : 180 mean,max change (kT/e) : 6.4348336E-04 1.2912750E-02 energy calculations done at 12.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.56000 DelPhi exited at 20:05:02 12.564u 0.230s 0:13.06 97.9% 0+0k 0+0io 0pf+0w