Sun Oct 9 22:32:45 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 Sun Oct 9 2011 at 22:32:45 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3108 !!! WARNING: SEP 397 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.5610009 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): -17.30200 42.77500 ymin,ymax (A): -5.811000 57.64700 zmin,zma (A): -5.212000 47.32100 x,y,z range (A): 60.07700 63.45800 52.53300 scale (grids/A): 0.5610009 object centre (A): 12.73650 25.91800 21.05450 number of atom coordinates read : 3108 total number of charged atoms : 3035 net assigned charge : 4.025009 assigned positive charge : 482.9420 centred at (gu) : 89.14773 88.27691 89.57042 assigned negative charge : -478.9179 centred at (gu) : 89.22587 88.21811 89.54315 start vw surface at 0.1100000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 6601 nv = 96 ne = 84 npr = 57875 no. pairs analyzed = 57875 no. exposed pairs = 4481 no. arc points = 32365 no. surface atoms = 1475 nbur = 1633 mkacc time = 9.9999994E-02 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= 329 mr = 3138 m= 0 mr = 7 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.2300000 number of dielectric boundary points 3785 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3272 ## 421 charges are in solution ## iepsmp to db, and charging done at 0.3000000 number of grid points assigned charge 8587 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.2264186E-10 7.0777401E-10 midg,1,midg; midg,igrid,midg -4.4334533E-10 7.7429108E-10 1,midg,midg; igrid,midg,midg 1.7254593E-09 -4.2017656E-10 gauss-seidel spectral radius is 0.9836345 estimated iterations to convergence 64 setup time was (sec) 0.4200000 now iterating at: 22:32:45 rms-change max change #iterations 8.6400658E-02 14.70797 at 10iterations 6.1409576E-03 0.9250355 at 20iterations 4.4707939E-04 8.5252762E-02 at 30iterations 3.9840827E-05 6.3209534E-03 at 40iterations 6.5511877E-06 8.5878372E-04 at 50iterations finished qdiffx linear iterations at : 22:32:48 total time elapsed so far: 3.310000 # loops : 50 mean,max change (kT/e) : 6.5511877E-06 8.5878372E-04 energy calculations done at 3.310000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.450000 DelPhi exited at 22:32:49 3.449u 0.161s 0:03.92 91.8% 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 Sun Oct 9 2011 at 22:32:49 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3108 !!! WARNING: SEP 397 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= 5.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.683003 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): -17.30200 42.77500 ymin,ymax (A): -5.811000 57.64700 zmin,zma (A): -5.212000 47.32100 x,y,z range (A): 60.07700 63.45800 52.53300 scale (grids/A): 1.683003 object centre (A): 12.73650 25.91800 21.05450 number of atom coordinates read : 3108 total number of charged atoms : 3035 net assigned charge : 4.025009 assigned positive charge : 482.9420 centred at (gu) : 87.44231 84.83040 88.71066 assigned negative charge : -478.9179 centred at (gu) : 87.67690 84.65395 88.62883 start vw surface at 0.1000000 fill in re-entrant regions at 0.1700000 boundary points on vw surface= 72092 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32365 grid for indexing accessible points = 1.400000 m= 22582 mr = 46178 m= 2738 mr = 14968 m= 120 mr = 1259 m= 1 mr = 21 m= 0 mr = 0 time to grow re-entrant surface = 0.1600000 no. cavity mid-points inaccessible to solvent = 238 time to turn everything in is 0.3600000 number of dielectric boundary points 35107 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 323 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.4400000 number of grid points assigned charge 23412 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) : 0.5610009 object centre at (A) : 12.73650 25.91800 21.05450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -5.3639258E-03 4.0114485E-03 midg,1,midg; midg,igrid,midg 8.0048563E-03 -5.1787361E-03 1,midg,midg; igrid,midg,midg -2.1726943E-03 3.4835576E-03 gauss-seidel spectral radius is 0.9983360 estimated iterations to convergence 195 setup time was (sec) 0.5800000 now iterating at: 22:32:49 rms-change max change #iterations 3.695589 159.2138 at 10iterations 1.585752 52.83275 at 20iterations 0.6843018 26.43886 at 30iterations 0.2939763 11.28068 at 40iterations 0.1266052 4.479496 at 50iterations 5.4709073E-02 1.886908 at 60iterations 2.3635108E-02 0.8602428 at 70iterations 1.0219106E-02 0.3458395 at 80iterations 4.4101463E-03 0.1510315 at 90iterations 1.9084056E-03 6.9568634E-02 at 100iterations 8.2582782E-04 3.0217171E-02 at 110iterations 3.5747202E-04 1.2954712E-02 at 120iterations finished qdiffx linear iterations at : 22:32:57 total time elapsed so far: 7.710000 # loops : 120 mean,max change (kT/e) : 3.5747202E-04 1.2954712E-02 energy calculations done at 7.710000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.840000 DelPhi exited at 22:32:57 7.842u 0.199s 0:08.39 95.7% 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 Sun Oct 9 2011 at 22:32:57 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: 281 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3108 !!! WARNING: SEP 397 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= 5.0000001E-02 grid size : 179 scale,in grids/A, set to be: 2.524504 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): -17.30200 42.77500 ymin,ymax (A): -5.811000 57.64700 zmin,zma (A): -5.212000 47.32100 x,y,z range (A): 60.07700 63.45800 52.53300 scale (grids/A): 2.524504 object centre (A): 12.73650 25.91800 21.05450 number of atom coordinates read : 3108 total number of charged atoms : 3035 net assigned charge : 4.025009 assigned positive charge : 482.9420 centred at (gu) : 86.16338 82.24536 88.06582 assigned negative charge : -478.9179 centred at (gu) : 86.51533 81.98074 87.94305 start vw surface at 9.0000004E-02 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 167261 reading accessible surface arcs data from file ARCDAT no. of arc points read = 32365 grid for indexing accessible points = 1.400000 m= 76474 mr = 114019 m= 23096 mr = 58693 m= 4369 mr = 16745 m= 434 mr = 2686 m= 14 mr = 194 m= 0 mr = 4 time to grow re-entrant surface = 0.5000000 no. cavity mid-points inaccessible to solvent = 837 time to turn everything in is 0.8800000 number of dielectric boundary points 79307 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 16 iepsmp to db, and charging done at 0.9700000 number of grid points assigned charge 24266 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) : 1.683003 object centre at (A) : 12.73650 25.91800 21.05450 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -0.1274489 6.7309611E-02 midg,1,midg; midg,igrid,midg 3.9633349E-02 -0.1949309 1,midg,midg; igrid,midg,midg -0.1702076 3.0581348E-02 gauss-seidel spectral radius is 0.9992014 estimated iterations to convergence 279 setup time was (sec) 1.120000 now iterating at: 22:32:58 rms-change max change #iterations 9.617096 337.9484 at 10iterations 5.611167 168.7220 at 20iterations 3.255085 85.75602 at 30iterations 1.869698 43.50674 at 40iterations 1.072411 26.17794 at 50iterations 0.6106445 14.27100 at 60iterations 0.3478023 7.353668 at 70iterations 0.1973307 4.221889 at 80iterations 0.1117510 2.296354 at 90iterations 6.3127376E-02 1.261627 at 100iterations 3.5686459E-02 0.7494581 at 110iterations 2.0116406E-02 0.4412785 at 120iterations 1.1352834E-02 0.2482471 at 130iterations 6.4025749E-03 0.1241775 at 140iterations 3.6015641E-03 7.2722673E-02 at 150iterations 2.0299386E-03 4.4027209E-02 at 160iterations 1.1410181E-03 2.1615982E-02 at 170iterations 6.4294250E-04 1.3421059E-02 at 180iterations finished qdiffx linear iterations at : 22:33:10 total time elapsed so far: 12.55000 # loops : 180 mean,max change (kT/e) : 6.4294250E-04 1.3421059E-02 energy calculations done at 12.55000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.68000 DelPhi exited at 22:33:10 12.685u 0.206s 0:13.26 97.1% 0+0k 0+0io 0pf+0w