Sun Oct 9 22:50:16 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 22:50:16 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 = 2177 !!! WARNING: SEP 108 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: 0.6329902 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): 0.9620000 50.33900 ymin,ymax (A): 0.9350001 57.17600 zmin,zma (A): -6.809000 33.53100 x,y,z range (A): 49.37700 56.24100 40.34000 scale (grids/A): 0.6329902 object centre (A): 25.65050 29.05550 13.36100 number of atom coordinates read : 2177 total number of charged atoms : 2036 net assigned charge : 3.025004 assigned positive charge : 323.6166 centred at (gu) : 88.85542 90.38760 90.43131 assigned negative charge : -320.5919 centred at (gu) : 89.01479 90.53206 90.29478 start vw surface at 0.1500000 fill in re-entrant regions at 0.1500000 boundary points on vw surface= 5977 nv = 96 ne = 84 npr = 42665 no. pairs analyzed = 42665 no. exposed pairs = 2850 no. arc points = 20031 no. surface atoms = 964 nbur = 1213 mkacc time = 0.1100000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 340 mr = 3178 m= 1 mr = 30 m= 0 mr = 0 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 16 time to turn everything in is 0.2900000 number of dielectric boundary points 3110 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1906 ## 202 charges are in solution ## iepsmp to db, and charging done at 0.4600000 number of grid points assigned charge 7036 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -6.8489934E-09 1.5518159E-08 midg,1,midg; midg,igrid,midg 1.3548235E-08 -8.9516270E-09 1,midg,midg; igrid,midg,midg 2.0410676E-08 -7.2945538E-09 gauss-seidel spectral radius is 0.9870387 estimated iterations to convergence 72 setup time was (sec) 0.6100000 now iterating at: 22:50:17 rms-change max change #iterations 0.1263967 19.55853 at 10iterations 1.2195790E-02 1.978563 at 20iterations 1.2366927E-03 0.1892209 at 30iterations 2.0818495E-04 3.9556980E-02 at 40iterations 7.7833458E-05 1.6582966E-02 at 50iterations finished qdiffx linear iterations at : 22:50:21 total time elapsed so far: 4.150000 # loops : 50 mean,max change (kT/e) : 7.7833458E-05 1.6582966E-02 energy calculations done at 4.150000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.330000 DelPhi exited at 22:50:21 4.333u 0.296s 0:04.90 94.2% 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 Sun Oct 9 2011 at 22:50:21 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 = 2177 !!! WARNING: SEP 108 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: 1.898970 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): 0.9620000 50.33900 ymin,ymax (A): 0.9350001 57.17600 zmin,zma (A): -6.809000 33.53100 x,y,z range (A): 49.37700 56.24100 40.34000 scale (grids/A): 1.898970 object centre (A): 25.65050 29.05550 13.36100 number of atom coordinates read : 2177 total number of charged atoms : 2036 net assigned charge : 3.025004 assigned positive charge : 323.6166 centred at (gu) : 86.56586 91.16261 91.29359 assigned negative charge : -320.5919 centred at (gu) : 87.04445 91.59610 90.88433 start vw surface at 0.1500000 fill in re-entrant regions at 0.2600000 boundary points on vw surface= 64453 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20031 grid for indexing accessible points = 1.400000 m= 21862 mr = 43694 m= 3236 mr = 15625 m= 197 mr = 1893 m= 3 mr = 66 m= 0 mr = 0 time to grow re-entrant surface = 0.2800000 no. cavity mid-points inaccessible to solvent = 304 time to turn everything in is 0.5800000 number of dielectric boundary points 28473 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 146 iepsmp to db, and charging done at 0.7200000 number of grid points assigned charge 16006 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) : 0.6329902 object centre at (A) : 25.65050 29.05550 13.36100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.6953990E-03 1.3060027E-02 midg,1,midg; midg,igrid,midg -7.2378558E-03 -9.7717885E-03 1,midg,midg; igrid,midg,midg 3.7527125E-02 1.4625234E-02 gauss-seidel spectral radius is 0.9985892 estimated iterations to convergence 211 setup time was (sec) 0.9300000 now iterating at: 22:50:22 rms-change max change #iterations 3.781548 164.3603 at 10iterations 1.756247 64.06714 at 20iterations 0.8127927 27.89789 at 30iterations 0.3769667 12.74609 at 40iterations 0.1748752 6.570269 at 50iterations 8.0806479E-02 2.793030 at 60iterations 3.7461571E-02 1.344191 at 70iterations 1.7397502E-02 0.6078920 at 80iterations 8.0474447E-03 0.2808938 at 90iterations 3.7360678E-03 0.1232510 at 100iterations 1.7291417E-03 5.7435036E-02 at 110iterations 8.0832432E-04 2.7746201E-02 at 120iterations finished qdiffx linear iterations at : 22:50:31 total time elapsed so far: 9.660000 # loops : 120 mean,max change (kT/e) : 8.0832432E-04 2.7746201E-02 energy calculations done at 9.660000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.850000 DelPhi exited at 22:50:32 9.849u 0.323s 0:10.46 97.1% 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 22:50:32 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 = 2177 !!! WARNING: SEP 108 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: 2.848456 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): 0.9620000 50.33900 ymin,ymax (A): 0.9350001 57.17600 zmin,zma (A): -6.809000 33.53100 x,y,z range (A): 49.37700 56.24100 40.34000 scale (grids/A): 2.848456 object centre (A): 25.65050 29.05550 13.36100 number of atom coordinates read : 2177 total number of charged atoms : 2036 net assigned charge : 3.025004 assigned positive charge : 323.6166 centred at (gu) : 84.84872 91.74385 91.94043 assigned negative charge : -320.5919 centred at (gu) : 85.56670 92.39420 91.32647 start vw surface at 0.1400000 fill in re-entrant regions at 0.4400000 boundary points on vw surface= 149249 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20031 grid for indexing accessible points = 1.400000 m= 72483 mr = 106521 m= 24539 mr = 58201 m= 5639 mr = 19162 m= 795 mr = 4076 m= 33 mr = 521 m= 0 mr = 11 time to grow re-entrant surface = 0.7400000 no. cavity mid-points inaccessible to solvent = 1056 time to turn everything in is 1.280000 number of dielectric boundary points 64246 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.440000 number of grid points assigned charge 16288 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) : 1.898970 object centre at (A) : 25.65050 29.05550 13.36100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -2.2097474E-02 0.1174709 midg,1,midg; midg,igrid,midg -0.2137080 5.1907562E-02 1,midg,midg; igrid,midg,midg 0.4156815 0.2323226 gauss-seidel spectral radius is 0.9992440 estimated iterations to convergence 287 setup time was (sec) 1.660000 now iterating at: 22:50:34 rms-change max change #iterations 9.047815 333.7573 at 10iterations 5.292765 137.1755 at 20iterations 3.067131 64.95799 at 30iterations 1.772878 37.67278 at 40iterations 1.021938 23.09148 at 50iterations 0.5880018 12.36677 at 60iterations 0.3369715 7.408577 at 70iterations 0.1931072 3.823937 at 80iterations 0.1110024 2.499177 at 90iterations 6.3516296E-02 1.334406 at 100iterations 3.6369648E-02 0.7726593 at 110iterations 2.0816818E-02 0.4663037 at 120iterations 1.1910145E-02 0.2397499 at 130iterations 6.8033799E-03 0.1427684 at 140iterations 3.8933815E-03 7.7223778E-02 at 150iterations 2.2311187E-03 4.4447899E-02 at 160iterations 1.2791359E-03 2.7755737E-02 at 170iterations 7.4097334E-04 1.5408993E-02 at 180iterations finished qdiffx linear iterations at : 22:50:48 total time elapsed so far: 15.71000 # loops : 180 mean,max change (kT/e) : 7.4097334E-04 1.5408993E-02 energy calculations done at 15.71000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.89000 DelPhi exited at 22:50:48 15.895u 0.320s 0:16.50 98.2% 0+0k 0+0io 0pf+0w