Sat Oct 8 11:35:58 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 11:35:58 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3345 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: 0.6354193 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): 31.32400 82.00300 ymin,ymax (A): 24.65800 80.68400 zmin,zma (A): -3.306000 46.05200 x,y,z range (A): 50.67900 56.02600 49.35800 scale (grids/A): 0.6354193 object centre (A): 56.66350 52.67100 21.37300 number of atom coordinates read : 3345 total number of charged atoms : 3193 net assigned charge : -5.499964 assigned positive charge : 508.1114 centred at (gu) : 90.32182 89.55413 91.32687 assigned negative charge : -513.6124 centred at (gu) : 90.14251 89.63368 91.33573 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 8541 nv = 96 ne = 84 npr = 72302 no. pairs analyzed = 72302 no. exposed pairs = 3614 no. arc points = 24683 no. surface atoms = 1231 nbur = 2114 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 468 mr = 5134 m= 0 mr = 75 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 186 time to turn everything in is 0.3600000 number of dielectric boundary points 3800 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2484 ## 238 charges are in solution ## iepsmp to db, and charging done at 0.4900000 number of grid points assigned charge 10749 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -4.4947424E-09 -1.0991838E-08 midg,1,midg; midg,igrid,midg 4.0365005E-09 -1.6361234E-08 1,midg,midg; igrid,midg,midg -2.9800001E-08 1.8061412E-08 gauss-seidel spectral radius is 0.9872174 estimated iterations to convergence 72 setup time was (sec) 0.6500000 now iterating at: 11:35:59 rms-change max change #iterations 0.1670653 24.11606 at 10iterations 1.6239695E-02 2.269859 at 20iterations 1.6133972E-03 0.2193683 at 30iterations 1.5900526E-04 1.9145966E-02 at 40iterations 1.5644255E-05 2.1495819E-03 at 50iterations finished qdiffx linear iterations at : 11:36:02 total time elapsed so far: 4.290000 # loops : 50 mean,max change (kT/e) : 1.5644255E-05 2.1495819E-03 energy calculations done at 4.290000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.480000 DelPhi exited at 11:36:03 4.482u 0.226s 0:05.20 90.3% 0+0k 0+0io 4pf+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 11:36:03 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 = 3345 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: 1.906258 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): 31.32400 82.00300 ymin,ymax (A): 24.65800 80.68400 zmin,zma (A): -3.306000 46.05200 x,y,z range (A): 50.67900 56.02600 49.35800 scale (grids/A): 1.906258 object centre (A): 56.66350 52.67100 21.37300 number of atom coordinates read : 3345 total number of charged atoms : 3193 net assigned charge : -5.499964 assigned positive charge : 508.1114 centred at (gu) : 90.96500 88.66178 93.97944 assigned negative charge : -513.6124 centred at (gu) : 90.42702 88.90063 94.00674 start vw surface at 0.1500000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 93138 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24683 grid for indexing accessible points = 1.400000 m= 34939 mr = 68001 m= 5751 mr = 27130 m= 337 mr = 3961 m= 5 mr = 141 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 8130 time to turn everything in is 0.6700000 number of dielectric boundary points 34937 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 159 iepsmp to db, and charging done at 0.8100000 number of grid points assigned charge 25117 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) : 0.6354193 object centre at (A) : 56.66350 52.67100 21.37300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -1.3378152E-02 -3.8563449E-02 midg,1,midg; midg,igrid,midg 1.2977131E-02 -2.9747002E-02 1,midg,midg; igrid,midg,midg -4.9021214E-02 6.9614360E-03 gauss-seidel spectral radius is 0.9986875 estimated iterations to convergence 219 setup time was (sec) 1.010000 now iterating at: 11:36:04 rms-change max change #iterations 4.958457 206.9955 at 10iterations 2.352392 66.16186 at 20iterations 1.121716 30.47439 at 30iterations 0.5338066 14.31508 at 40iterations 0.2539679 7.671600 at 50iterations 0.1210655 3.450713 at 60iterations 5.7684332E-02 1.780112 at 70iterations 2.7504480E-02 0.7470055 at 80iterations 1.3075527E-02 0.3728409 at 90iterations 6.2432298E-03 0.1832476 at 100iterations 2.9681097E-03 8.2988739E-02 at 110iterations 1.4156833E-03 4.1469574E-02 at 120iterations finished qdiffx linear iterations at : 11:36:13 total time elapsed so far: 9.770000 # loops : 120 mean,max change (kT/e) : 1.4156833E-03 4.1469574E-02 energy calculations done at 9.770000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.950000 DelPhi exited at 11:36:13 9.954u 0.269s 0:10.48 97.4% 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 11:36:14 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 = 3345 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: 2.859387 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): 31.32400 82.00300 ymin,ymax (A): 24.65800 80.68400 zmin,zma (A): -3.306000 46.05200 x,y,z range (A): 50.67900 56.02600 49.35800 scale (grids/A): 2.859387 object centre (A): 56.66350 52.67100 21.37300 number of atom coordinates read : 3345 total number of charged atoms : 3193 net assigned charge : -5.499964 assigned positive charge : 508.1114 centred at (gu) : 91.44733 87.99220 95.96872 assigned negative charge : -513.6124 centred at (gu) : 90.64037 88.35075 96.01001 start vw surface at 0.1600000 fill in re-entrant regions at 0.5900000 boundary points on vw surface= 215626 reading accessible surface arcs data from file ARCDAT no. of arc points read = 24683 grid for indexing accessible points = 1.400000 m= 112069 mr = 163955 m= 42454 mr = 94390 m= 10519 mr = 35774 m= 1590 mr = 8355 m= 133 mr = 1149 m= 1 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 1.040000 no. cavity mid-points inaccessible to solvent = 28456 time to turn everything in is 1.770000 number of dielectric boundary points 78696 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.930000 number of grid points assigned charge 25544 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) : 1.906258 object centre at (A) : 56.66350 52.67100 21.37300 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1420468 -0.3492946 midg,1,midg; midg,igrid,midg 0.1765708 -0.2615417 1,midg,midg; igrid,midg,midg -0.4964914 6.7656292E-03 gauss-seidel spectral radius is 0.9992728 estimated iterations to convergence 293 setup time was (sec) 2.130000 now iterating at: 11:36:16 rms-change max change #iterations 11.33519 447.2235 at 10iterations 6.568261 123.9189 at 20iterations 3.807189 62.56915 at 30iterations 2.194328 34.28275 at 40iterations 1.269281 23.09138 at 50iterations 0.7331325 12.17815 at 60iterations 0.4233372 6.973823 at 70iterations 0.2440550 4.141392 at 80iterations 0.1412383 2.173000 at 90iterations 8.1349581E-02 1.358212 at 100iterations 4.6943519E-02 0.6919098 at 110iterations 2.7118264E-02 0.4380007 at 120iterations 1.5642449E-02 0.2457833 at 130iterations 9.0413382E-03 0.1436539 at 140iterations 5.2077849E-03 8.1116676E-02 at 150iterations 3.0058299E-03 4.8550606E-02 at 160iterations 1.7373601E-03 2.8586388E-02 at 170iterations 1.0039981E-03 1.6288757E-02 at 180iterations finished qdiffx linear iterations at : 11:36:30 total time elapsed so far: 16.00000 # loops : 180 mean,max change (kT/e) : 1.0039981E-03 1.6288757E-02 energy calculations done at 16.00000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 16.18000 DelPhi exited at 11:36:30 16.181u 0.296s 0:16.75 98.3% 0+0k 0+0io 0pf+0w