Sat Oct 15 13:39:04 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 Sat Oct 15 2011 at 13:39:04 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3630 !!! WARNING: GLM 287 has a net charge of -0.0940 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: 0.5971852 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): -53.07900 6.534000 ymin,ymax (A): -30.59500 25.99800 zmin,zma (A): -16.29900 41.62700 x,y,z range (A): 59.61300 56.59300 57.92600 scale (grids/A): 0.5971852 object centre (A): -23.27250 -2.298500 12.66400 number of atom coordinates read : 3630 total number of charged atoms : 3517 net assigned charge : -10.09400 assigned positive charge : 574.3717 centred at (gu) : 89.43039 90.69375 90.22168 assigned negative charge : -584.4679 centred at (gu) : 89.47733 90.55402 90.37202 start vw surface at 0.1000000 fill in re-entrant regions at 0.1100000 boundary points on vw surface= 8605 nv = 96 ne = 84 npr = 71728 no. pairs analyzed = 71728 no. exposed pairs = 4433 no. arc points = 30808 no. surface atoms = 1485 nbur = 2145 mkacc time = 0.1200000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 393 mr = 4828 m= 1 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.1400000 no. cavity mid-points inaccessible to solvent = 155 time to turn everything in is 0.2500000 number of dielectric boundary points 4127 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3071 ## 314 charges are in solution ## iepsmp to db, and charging done at 0.3200000 number of grid points assigned charge 10850 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 3.2734213E-09 -1.2291848E-08 midg,1,midg; midg,igrid,midg -9.5073096E-09 3.4926337E-09 1,midg,midg; igrid,midg,midg -1.8327934E-09 -5.5955112E-09 gauss-seidel spectral radius is 0.9855716 estimated iterations to convergence 68 setup time was (sec) 0.4400000 now iterating at: 13:39:05 rms-change max change #iterations 0.1278985 17.56731 at 10iterations 1.0967945E-02 1.703919 at 20iterations 9.3561778E-04 0.1302500 at 30iterations 8.1730774E-05 1.1829376E-02 at 40iterations 1.0101911E-05 1.7805099E-03 at 50iterations finished qdiffx linear iterations at : 13:39:09 total time elapsed so far: 3.630000 # loops : 50 mean,max change (kT/e) : 1.0101911E-05 1.7805099E-03 energy calculations done at 3.630000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.760000 DelPhi exited at 13:39:09 3.767u 0.231s 0:05.37 74.3% 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 Sat Oct 15 2011 at 13:39:09 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3630 !!! WARNING: GLM 287 has a net charge of -0.0940 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: 1.791556 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): -53.07900 6.534000 ymin,ymax (A): -30.59500 25.99800 zmin,zma (A): -16.29900 41.62700 x,y,z range (A): 59.61300 56.59300 57.92600 scale (grids/A): 1.791556 object centre (A): -23.27250 -2.298500 12.66400 number of atom coordinates read : 3630 total number of charged atoms : 3517 net assigned charge : -10.09400 assigned positive charge : 574.3717 centred at (gu) : 88.29051 92.08003 90.66383 assigned negative charge : -584.4679 centred at (gu) : 88.43169 91.66169 91.11591 start vw surface at 0.1000000 fill in re-entrant regions at 0.2000000 boundary points on vw surface= 94449 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30808 grid for indexing accessible points = 1.400000 m= 32525 mr = 67049 m= 4313 mr = 23560 m= 172 mr = 2429 m= 1 mr = 44 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 5214 time to turn everything in is 0.4500000 number of dielectric boundary points 38378 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 269 ## 2 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 27429 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) : 0.5971852 object centre at (A) : -23.27250 -2.298500 12.66400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 9.4624907E-03 -7.6923244E-02 midg,1,midg; midg,igrid,midg -3.2994770E-02 3.8836042E-03 1,midg,midg; igrid,midg,midg -7.4744783E-02 -4.4153236E-02 gauss-seidel spectral radius is 0.9985606 estimated iterations to convergence 209 setup time was (sec) 0.6800000 now iterating at: 13:39:10 rms-change max change #iterations 4.737626 171.8039 at 10iterations 2.162748 77.89418 at 20iterations 0.9920538 32.90643 at 30iterations 0.4547889 15.12042 at 40iterations 0.2092423 6.383057 at 50iterations 9.5782198E-02 3.006104 at 60iterations 4.3787450E-02 1.221703 at 70iterations 2.0226128E-02 0.5982590 at 80iterations 9.2948703E-03 0.2673626 at 90iterations 4.2823534E-03 0.1254444 at 100iterations 1.9603979E-03 5.7078838E-02 at 110iterations 9.0151647E-04 2.8475761E-02 at 120iterations finished qdiffx linear iterations at : 13:39:19 total time elapsed so far: 8.450000 # loops : 120 mean,max change (kT/e) : 9.0151647E-04 2.8475761E-02 energy calculations done at 8.450000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.590000 DelPhi exited at 13:39:20 8.590u 0.272s 0:10.58 83.7% 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 Sat Oct 15 2011 at 13:39:20 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: 297 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3630 !!! WARNING: GLM 287 has a net charge of -0.0940 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: 2.687333 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): -53.07900 6.534000 ymin,ymax (A): -30.59500 25.99800 zmin,zma (A): -16.29900 41.62700 x,y,z range (A): 59.61300 56.59300 57.92600 scale (grids/A): 2.687333 object centre (A): -23.27250 -2.298500 12.66400 number of atom coordinates read : 3630 total number of charged atoms : 3517 net assigned charge : -10.09400 assigned positive charge : 574.3717 centred at (gu) : 87.43552 93.11974 90.99549 assigned negative charge : -584.4679 centred at (gu) : 87.64745 92.49258 91.67374 start vw surface at 0.1000000 fill in re-entrant regions at 0.3800000 boundary points on vw surface= 219111 reading accessible surface arcs data from file ARCDAT no. of arc points read = 30808 grid for indexing accessible points = 1.400000 m= 108319 mr = 162793 m= 35569 mr = 88224 m= 7367 mr = 27890 m= 803 mr = 5279 m= 24 mr = 500 m= 0 mr = 0 time to grow re-entrant surface = 0.6700000 no. cavity mid-points inaccessible to solvent = 17259 time to turn everything in is 1.150000 number of dielectric boundary points 86507 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 8 iepsmp to db, and charging done at 1.260000 number of grid points assigned charge 28130 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) : 1.791556 object centre at (A) : -23.27250 -2.298500 12.66400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.1390055 -1.100467 midg,1,midg; midg,igrid,midg -0.3202270 3.1027395E-02 1,midg,midg; igrid,midg,midg -0.9602074 -0.6980829 gauss-seidel spectral radius is 0.9992638 estimated iterations to convergence 291 setup time was (sec) 1.420000 now iterating at: 13:39:22 rms-change max change #iterations 11.41057 273.7835 at 10iterations 6.730245 138.4243 at 20iterations 3.942246 81.40116 at 30iterations 2.292978 44.63547 at 40iterations 1.328235 25.09211 at 50iterations 0.7703933 12.76053 at 60iterations 0.4455813 7.387153 at 70iterations 0.2577602 4.858558 at 80iterations 0.1485088 2.513329 at 90iterations 8.5566431E-02 1.544575 at 100iterations 4.9433883E-02 0.9610119 at 110iterations 2.8434653E-02 0.4673729 at 120iterations 1.6354546E-02 0.2631290 at 130iterations 9.4469460E-03 0.1606712 at 140iterations 5.4466748E-03 8.6585999E-02 at 150iterations 3.1465511E-03 4.9606323E-02 at 160iterations 1.8263003E-03 3.0588627E-02 at 170iterations 1.0696624E-03 1.8718719E-02 at 180iterations finished qdiffx linear iterations at : 13:39:40 total time elapsed so far: 13.82000 # loops : 180 mean,max change (kT/e) : 1.0696624E-03 1.8718719E-02 energy calculations done at 13.82000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 13.95000 DelPhi exited at 13:39:41 13.948u 0.266s 0:21.22 66.9% 0+0k 0+0io 0pf+0w