Tue Oct 11 07:48:19 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 07:48:19 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2679 !!! WARNING: SEP 206 has a net charge of -0.4750 !!! WARNING: SEP 211 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.6360550 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): -13.32300 42.64700 ymin,ymax (A): -22.41500 25.32200 zmin,zma (A): -5.482000 40.33000 x,y,z range (A): 55.97000 47.73700 45.81200 scale (grids/A): 0.6360550 object centre (A): 14.66200 1.453501 17.42400 number of atom coordinates read : 2679 total number of charged atoms : 2318 net assigned charge : 5.550004 assigned positive charge : 370.6413 centred at (gu) : 89.58755 88.85513 89.31145 assigned negative charge : -365.0917 centred at (gu) : 89.67270 88.82385 89.46485 start vw surface at 0.1600000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 6581 nv = 96 ne = 84 npr = 50305 no. pairs analyzed = 50305 no. exposed pairs = 2889 no. arc points = 19819 no. surface atoms = 997 nbur = 1682 mkacc time = 0.1400000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 318 mr = 3758 m= 2 mr = 41 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 3102 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2026 ## 215 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7950 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 2.5458155E-08 -7.0414532E-09 midg,1,midg; midg,igrid,midg 5.0398583E-09 7.9945437E-09 1,midg,midg; igrid,midg,midg 1.6817514E-08 -1.2051179E-09 gauss-seidel spectral radius is 0.9871753 estimated iterations to convergence 72 setup time was (sec) 0.6100000 now iterating at: 07:48:20 rms-change max change #iterations 0.1400680 21.52083 at 10iterations 1.4553481E-02 2.297258 at 20iterations 1.6905671E-03 0.2818718 at 30iterations 2.4444470E-04 3.3355713E-02 at 40iterations 4.3796168E-05 6.5078735E-03 at 50iterations finished qdiffx linear iterations at : 07:48:23 total time elapsed so far: 3.880000 # loops : 50 mean,max change (kT/e) : 4.3796168E-05 6.5078735E-03 energy calculations done at 3.880000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.060000 DelPhi exited at 07:48:24 4.064u 0.253s 0:04.77 90.3% 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 07:48:24 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2679 !!! WARNING: SEP 206 has a net charge of -0.4750 !!! WARNING: SEP 211 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.908165 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): -13.32300 42.64700 ymin,ymax (A): -22.41500 25.32200 zmin,zma (A): -5.482000 40.33000 x,y,z range (A): 55.97000 47.73700 45.81200 scale (grids/A): 1.908165 object centre (A): 14.66200 1.453501 17.42400 number of atom coordinates read : 2679 total number of charged atoms : 2318 net assigned charge : 5.550004 assigned positive charge : 370.6413 centred at (gu) : 88.76193 86.56520 87.93367 assigned negative charge : -365.0917 centred at (gu) : 89.01804 86.47144 88.39429 start vw surface at 0.1700000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 70984 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19819 grid for indexing accessible points = 1.400000 m= 26048 mr = 50456 m= 3856 mr = 19718 m= 188 mr = 2367 m= 5 mr = 73 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.6500000 number of dielectric boundary points 28467 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 135 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 18217 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) : 0.6360550 object centre at (A) : 14.66200 1.453501 17.42400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.8872477E-02 -6.6988487E-03 midg,1,midg; midg,igrid,midg 3.7149005E-03 1.8579632E-02 1,midg,midg; igrid,midg,midg 1.8895974E-02 6.6914856E-03 gauss-seidel spectral radius is 0.9986181 estimated iterations to convergence 213 setup time was (sec) 0.9300000 now iterating at: 07:48:25 rms-change max change #iterations 4.101038 164.9356 at 10iterations 1.921212 67.85024 at 20iterations 0.8943805 30.31797 at 30iterations 0.4190323 14.11004 at 40iterations 0.1967935 7.036087 at 50iterations 9.2085563E-02 2.872690 at 60iterations 4.3085560E-02 1.371983 at 70iterations 2.0201588E-02 0.6334267 at 80iterations 9.5104864E-03 0.2944260 at 90iterations 4.4903383E-03 0.1409056 at 100iterations 2.1470867E-03 7.1868896E-02 at 110iterations 1.0394464E-03 3.3560276E-02 at 120iterations finished qdiffx linear iterations at : 07:48:34 total time elapsed so far: 9.150000 # loops : 120 mean,max change (kT/e) : 1.0394464E-03 3.3560276E-02 energy calculations done at 9.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.320000 DelPhi exited at 07:48:34 9.327u 0.299s 0:10.15 94.6% 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 Tue Oct 11 2011 at 07:48:34 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: 282 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2679 !!! WARNING: SEP 206 has a net charge of -0.4750 !!! WARNING: SEP 211 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.862247 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): -13.32300 42.64700 ymin,ymax (A): -22.41500 25.32200 zmin,zma (A): -5.482000 40.33000 x,y,z range (A): 55.97000 47.73700 45.81200 scale (grids/A): 2.862247 object centre (A): 14.66200 1.453501 17.42400 number of atom coordinates read : 2679 total number of charged atoms : 2318 net assigned charge : 5.550004 assigned positive charge : 370.6413 centred at (gu) : 88.14281 84.84766 86.90044 assigned negative charge : -365.0917 centred at (gu) : 88.52698 84.70712 87.59139 start vw surface at 0.1600000 fill in re-entrant regions at 0.5500000 boundary points on vw surface= 163884 reading accessible surface arcs data from file ARCDAT no. of arc points read = 19819 grid for indexing accessible points = 1.400000 m= 84792 mr = 121603 m= 30192 mr = 70649 m= 6674 mr = 24532 m= 890 mr = 4969 m= 51 mr = 615 m= 0 mr = 24 time to grow re-entrant surface = 0.9800000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.640000 number of dielectric boundary points 64091 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 0 iepsmp to db, and charging done at 1.780000 number of grid points assigned charge 18537 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) : 1.908165 object centre at (A) : 14.66200 1.453501 17.42400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3701317 -0.1309098 midg,1,midg; midg,igrid,midg 4.3623321E-02 0.2064917 1,midg,midg; igrid,midg,midg 6.4698167E-02 1.5535559E-02 gauss-seidel spectral radius is 0.9992427 estimated iterations to convergence 287 setup time was (sec) 1.960000 now iterating at: 07:48:37 rms-change max change #iterations 9.555407 334.2970 at 10iterations 5.519351 116.8335 at 20iterations 3.182227 66.92294 at 30iterations 1.830791 35.09215 at 40iterations 1.049150 21.52944 at 50iterations 0.6016043 10.80535 at 60iterations 0.3453192 6.600780 at 70iterations 0.1977081 3.672565 at 80iterations 0.1129515 2.145489 at 90iterations 6.4695351E-02 1.326168 at 100iterations 3.6978349E-02 0.6995535 at 110iterations 2.1158703E-02 0.4392128 at 120iterations 1.2167769E-02 0.2353172 at 130iterations 7.0003127E-03 0.1206844 at 140iterations 4.0722704E-03 7.2052002E-02 at 150iterations 2.3895078E-03 4.3090820E-02 at 160iterations 1.4285512E-03 2.5779724E-02 at 170iterations 8.7797362E-04 1.6258240E-02 at 180iterations finished qdiffx linear iterations at : 07:48:50 total time elapsed so far: 15.37000 # loops : 180 mean,max change (kT/e) : 8.7797362E-04 1.6258240E-02 energy calculations done at 15.37000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.56000 DelPhi exited at 07:48:51 15.557u 0.305s 0:16.36 96.8% 0+0k 0+0io 0pf+0w