Tue Oct 11 03:19:24 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 Tue Oct 11 2011 at 03:19:25 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3516 !!! WARNING: ARG 336 has a net charge of 1.5000 !!! WARNING: ARG 672 has a net charge of 1.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5407950 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): -7.522000 46.50800 ymin,ymax (A): 72.34000 138.1690 zmin,zma (A): 103.1390 163.3770 x,y,z range (A): 54.03000 65.82901 60.23800 scale (grids/A): 0.5407950 object centre (A): 19.49300 105.2545 133.2580 number of atom coordinates read : 3516 total number of charged atoms : 3375 net assigned charge : -4.499971 assigned positive charge : 535.6150 centred at (gu) : 91.06544 92.10058 91.89819 assigned negative charge : -540.1168 centred at (gu) : 91.08640 92.11407 91.87309 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6689 nv = 96 ne = 84 npr = 70896 no. pairs analyzed = 70896 no. exposed pairs = 4577 no. arc points = 32207 no. surface atoms = 1510 nbur = 2006 mkacc time = 0.1200000 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 = 1.596000 m= 262 mr = 3409 m= 3 mr = 10 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2500000 number of dielectric boundary points 3535 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3293 ## 421 charges are in solution ## iepsmp to db, and charging done at 0.3100000 number of grid points assigned charge 8881 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -2.4565414E-10 -9.1680809E-11 midg,1,midg; midg,igrid,midg -8.4222296E-11 -5.2963994E-10 1,midg,midg; igrid,midg,midg -6.9653096E-11 -4.7337728E-10 gauss-seidel spectral radius is 0.9824160 estimated iterations to convergence 62 setup time was (sec) 0.4400000 now iterating at: 03:19:25 rms-change max change #iterations 7.6898083E-02 13.26216 at 10iterations 5.2922331E-03 0.9219475 at 20iterations 5.7558087E-04 8.6729050E-02 at 30iterations 1.3623541E-04 1.9296169E-02 at 40iterations 3.9055114E-05 5.0024986E-03 at 50iterations finished qdiffx linear iterations at : 03:19:28 total time elapsed so far: 3.370000 # loops : 50 mean,max change (kT/e) : 3.9055114E-05 5.0024986E-03 energy calculations done at 3.370000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.510000 DelPhi exited at 03:19:29 3.514u 0.176s 0:03.99 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 Tue Oct 11 2011 at 03:19:29 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 = 3516 !!! WARNING: ARG 336 has a net charge of 1.5000 !!! WARNING: ARG 672 has a net charge of 1.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.622385 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): -7.522000 46.50800 ymin,ymax (A): 72.34000 138.1690 zmin,zma (A): 103.1390 163.3770 x,y,z range (A): 54.03000 65.82901 60.23800 scale (grids/A): 1.622385 object centre (A): 19.49300 105.2545 133.2580 number of atom coordinates read : 3516 total number of charged atoms : 3375 net assigned charge : -4.499971 assigned positive charge : 535.6150 centred at (gu) : 93.19582 96.30049 95.69376 assigned negative charge : -540.1168 centred at (gu) : 93.25872 96.34187 95.61885 start vw surface at 0.1200000 fill in re-entrant regions at 0.1900000 boundary points on vw surface= 74266 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32207 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 22805 mr = 50178 m= 2253 mr = 15334 m= 63 mr = 1005 m= 0 mr = 2 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 187 time to turn everything in is 0.3800000 number of dielectric boundary points 32868 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 441 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 25794 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) : 0.5407950 object centre at (A) : 19.49300 105.2545 133.2580 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -4.3153195E-03 4.0814560E-03 midg,1,midg; midg,igrid,midg 2.7435135E-02 -1.6589370E-02 1,midg,midg; igrid,midg,midg 7.9830298E-03 -3.4327866E-03 gauss-seidel spectral radius is 0.9982129 estimated iterations to convergence 188 setup time was (sec) 0.6100000 now iterating at: 03:19:29 rms-change max change #iterations 3.615492 152.2714 at 10iterations 1.510577 81.54795 at 20iterations 0.6334172 24.73879 at 30iterations 0.2650471 9.830439 at 40iterations 0.1112286 3.946558 at 50iterations 4.6700843E-02 1.481541 at 60iterations 1.9617299E-02 0.7122498 at 70iterations 8.3235111E-03 0.2849593 at 80iterations 3.5184459E-03 0.1150084 at 90iterations 1.5189522E-03 5.1805496E-02 at 100iterations 6.6975941E-04 2.2463799E-02 at 110iterations 3.0829440E-04 1.0624886E-02 at 120iterations finished qdiffx linear iterations at : 03:19:37 total time elapsed so far: 7.820000 # loops : 120 mean,max change (kT/e) : 3.0829440E-04 1.0624886E-02 energy calculations done at 7.820000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.960000 DelPhi exited at 03:19:37 7.962u 0.185s 0:08.53 95.4% 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 Tue Oct 11 2011 at 03:19:37 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: 236 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3516 !!! WARNING: ARG 336 has a net charge of 1.5000 !!! WARNING: ARG 672 has a net charge of 1.5000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.433578 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): -7.522000 46.50800 ymin,ymax (A): 72.34000 138.1690 zmin,zma (A): 103.1390 163.3770 x,y,z range (A): 54.03000 65.82901 60.23800 scale (grids/A): 2.433578 object centre (A): 19.49300 105.2545 133.2580 number of atom coordinates read : 3516 total number of charged atoms : 3375 net assigned charge : -4.499971 assigned positive charge : 535.6150 centred at (gu) : 94.79334 99.45039 98.54035 assigned negative charge : -540.1168 centred at (gu) : 94.88808 99.51253 98.42821 start vw surface at 0.1100000 fill in re-entrant regions at 0.3200000 boundary points on vw surface= 172722 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32207 initial cube size too small, in assigning accessible points to a grid therefore rescaling... grid for indexing accessible points = 1.484000 m= 79468 mr = 123352 m= 21860 mr = 61997 m= 3346 mr = 16037 m= 215 mr = 2027 m= 6 mr = 78 m= 0 mr = 0 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 624 time to turn everything in is 0.9000000 number of dielectric boundary points 74126 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 35 iepsmp to db, and charging done at 0.9900000 number of grid points assigned charge 26958 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) : 1.622385 object centre at (A) : 19.49300 105.2545 133.2580 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 1.2099476E-02 9.6739732E-02 midg,1,midg; midg,igrid,midg 0.6011370 -0.4018003 1,midg,midg; igrid,midg,midg 0.1234949 -3.7892532E-02 gauss-seidel spectral radius is 0.9991592 estimated iterations to convergence 272 setup time was (sec) 1.130000 now iterating at: 03:19:39 rms-change max change #iterations 9.536930 352.5476 at 10iterations 5.440233 141.8095 at 20iterations 3.080347 77.86344 at 30iterations 1.732302 38.66729 at 40iterations 0.9708715 25.89437 at 50iterations 0.5438798 13.44514 at 60iterations 0.3034991 7.442325 at 70iterations 0.1690169 3.527050 at 80iterations 9.4203249E-02 1.955990 at 90iterations 5.2380733E-02 1.057754 at 100iterations 2.9055910E-02 0.6274872 at 110iterations 1.6160209E-02 0.3226221 at 120iterations 8.9818081E-03 0.1946259 at 130iterations 5.0012656E-03 0.1095543 at 140iterations 2.7794156E-03 5.6355953E-02 at 150iterations 1.5515470E-03 2.9434204E-02 at 160iterations 8.7086490E-04 1.7151594E-02 at 170iterations 4.9270474E-04 9.1392994E-03 at 180iterations finished qdiffx linear iterations at : 03:19:50 total time elapsed so far: 12.43000 # loops : 180 mean,max change (kT/e) : 4.9270474E-04 9.1392994E-03 energy calculations done at 12.43000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.57000 DelPhi exited at 03:19:50 12.569u 0.212s 0:13.23 96.5% 0+0k 0+0io 0pf+0w