Mon Oct 10 16:03:36 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 Mon Oct 10 2011 at 16:03:36 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4732 !!! WARNING: ASP 610 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.5485785 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): 7.688000 62.81100 ymin,ymax (A): -29.67500 34.70800 zmin,zma (A): -29.21000 35.68500 x,y,z range (A): 55.12300 64.38300 64.89500 scale (grids/A): 0.5485785 object centre (A): 35.24950 2.516500 3.237499 number of atom coordinates read : 4732 total number of charged atoms : 4573 net assigned charge : 3.000012 assigned positive charge : 711.0806 centred at (gu) : 89.56377 89.91386 88.49362 assigned negative charge : -708.0850 centred at (gu) : 89.50983 89.86589 88.46256 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 9140 nv = 96 ne = 84 npr = 97161 no. pairs analyzed = 97161 no. exposed pairs = 5824 no. arc points = 39256 no. surface atoms = 1960 nbur = 2772 mkacc time = 0.2100000 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= 386 mr = 5004 m= 3 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.2400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.4500000 number of dielectric boundary points 4504 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4077 ## 490 charges are in solution ## iepsmp to db, and charging done at 0.5500000 number of grid points assigned charge 12120 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.2005477E-10 3.9852108E-10 midg,1,midg; midg,igrid,midg -3.5290440E-10 7.5424988E-10 1,midg,midg; igrid,midg,midg -4.6499396E-10 7.5338613E-10 gauss-seidel spectral radius is 0.9829920 estimated iterations to convergence 63 setup time was (sec) 0.6600000 now iterating at: 16:03:37 rms-change max change #iterations 9.6826054E-02 14.98169 at 10iterations 7.1968557E-03 1.181126 at 20iterations 1.2011747E-03 0.1951942 at 30iterations 4.6146111E-04 6.4357758E-02 at 40iterations 2.0056377E-04 2.4606705E-02 at 50iterations finished qdiffx linear iterations at : 16:03:40 total time elapsed so far: 3.100000 # loops : 50 mean,max change (kT/e) : 2.0056377E-04 2.4606705E-02 energy calculations done at 3.100000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.280000 DelPhi exited at 16:03:40 3.281u 0.152s 0:03.80 90.2% 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 Mon Oct 10 2011 at 16:03:40 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4732 !!! WARNING: ASP 610 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1400000 grid size : 179 scale,in grids/A, set to be: 1.645736 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): 7.688000 62.81100 ymin,ymax (A): -29.67500 34.70800 zmin,zma (A): -29.21000 35.68500 x,y,z range (A): 55.12300 64.38300 64.89500 scale (grids/A): 1.645736 object centre (A): 35.24950 2.516500 3.237499 number of atom coordinates read : 4732 total number of charged atoms : 4573 net assigned charge : 3.000012 assigned positive charge : 711.0806 centred at (gu) : 88.68935 89.73995 85.47932 assigned negative charge : -708.0850 centred at (gu) : 88.52879 89.59727 85.38730 start vw surface at 0.2200000 fill in re-entrant regions at 0.3400000 boundary points on vw surface= 101785 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39256 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.456000 m= 32745 mr = 72015 m= 3722 mr = 22947 m= 104 mr = 1871 m= 0 mr = 5 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 995 time to turn everything in is 0.7000000 number of dielectric boundary points 41518 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 414 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.8200000 number of grid points assigned charge 35119 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) : 0.5485785 object centre at (A) : 35.24950 2.516500 3.237499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.5646375E-03 -5.6851846E-03 midg,1,midg; midg,igrid,midg 1.3831391E-02 1.2832184E-02 1,midg,midg; igrid,midg,midg -1.3006909E-03 4.6490044E-03 gauss-seidel spectral radius is 0.9983836 estimated iterations to convergence 197 setup time was (sec) 0.9700000 now iterating at: 16:03:41 rms-change max change #iterations 4.404206 161.5396 at 10iterations 1.929296 58.06945 at 20iterations 0.8458206 24.62409 at 30iterations 0.3707244 11.89438 at 40iterations 0.1627919 4.405418 at 50iterations 7.1572490E-02 1.935362 at 60iterations 3.1512737E-02 0.9471397 at 70iterations 1.3966075E-02 0.4424725 at 80iterations 6.3012028E-03 0.1896820 at 90iterations 2.9347816E-03 0.1053066 at 100iterations 1.4636647E-03 4.9260139E-02 at 110iterations 8.3274423E-04 2.5829315E-02 at 120iterations finished qdiffx linear iterations at : 16:03:48 total time elapsed so far: 7.250000 # loops : 120 mean,max change (kT/e) : 8.3274423E-04 2.5829315E-02 energy calculations done at 7.250000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.420000 DelPhi exited at 16:03:48 7.424u 0.179s 0:07.88 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 Mon Oct 10 2011 at 16:03:48 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 4732 !!! WARNING: ASP 610 has a net charge of -2.0000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 0.1100000 grid size : 179 scale,in grids/A, set to be: 2.468603 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): 7.688000 62.81100 ymin,ymax (A): -29.67500 34.70800 zmin,zma (A): -29.21000 35.68500 x,y,z range (A): 55.12300 64.38300 64.89500 scale (grids/A): 2.468603 object centre (A): 35.24950 2.516500 3.237499 number of atom coordinates read : 4732 total number of charged atoms : 4573 net assigned charge : 3.000012 assigned positive charge : 711.0806 centred at (gu) : 88.03365 89.60947 83.21866 assigned negative charge : -708.0850 centred at (gu) : 87.79318 89.39578 83.08078 start vw surface at 0.2200000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 237095 reading accessible surface arcs data from file ARCDAT no. of arc points read = 39256 grid for indexing accessible points = 1.400000 m= 112403 mr = 176342 m= 33159 mr = 89732 m= 5907 mr = 25165 m= 490 mr = 3937 m= 17 mr = 202 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 0.9900001 no. cavity mid-points inaccessible to solvent = 3119 time to turn everything in is 1.720000 number of dielectric boundary points 93694 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 19 iepsmp to db, and charging done at 1.870000 number of grid points assigned charge 36536 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) : 1.645736 object centre at (A) : 35.24950 2.516500 3.237499 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1695171 -0.1271320 midg,1,midg; midg,igrid,midg 0.3091465 0.1198600 1,midg,midg; igrid,midg,midg 1.6001593E-02 8.1625246E-02 gauss-seidel spectral radius is 0.9992360 estimated iterations to convergence 286 setup time was (sec) 2.040000 now iterating at: 16:03:50 rms-change max change #iterations 11.42560 347.1313 at 10iterations 6.739441 160.8739 at 20iterations 3.942963 81.84155 at 30iterations 2.300655 44.87683 at 40iterations 1.335844 24.09092 at 50iterations 0.7728119 13.40274 at 60iterations 0.4451039 8.450525 at 70iterations 0.2570743 4.393768 at 80iterations 0.1478975 2.615260 at 90iterations 8.4897563E-02 1.627625 at 100iterations 4.8752084E-02 0.8546696 at 110iterations 2.7994707E-02 0.4551716 at 120iterations 1.6089307E-02 0.2863684 at 130iterations 9.2700999E-03 0.1681061 at 140iterations 5.3794957E-03 9.7838879E-02 at 150iterations 3.1601551E-03 5.7084084E-02 at 160iterations 1.9086356E-03 3.3981323E-02 at 170iterations 1.2027643E-03 2.0170212E-02 at 180iterations finished qdiffx linear iterations at : 16:04:01 total time elapsed so far: 12.88000 # loops : 180 mean,max change (kT/e) : 1.2027643E-03 2.0170212E-02 energy calculations done at 12.88000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.06000 DelPhi exited at 16:04:02 13.062u 0.228s 0:13.66 97.2% 0+0k 0+0io 0pf+0w