Mon Oct 10 14:01:49 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 Mon Oct 10 2011 at 14:01:49 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3203 !!! WARNING: SEP 64 has a net charge of -0.4750 !!! WARNING: GLM 120 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 0.5883033 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): -16.45200 34.17500 ymin,ymax (A): -1.758000 46.55000 zmin,zma (A): -6.288000 54.22500 x,y,z range (A): 50.62700 48.30800 60.51300 scale (grids/A): 0.5883033 object centre (A): 8.861502 22.39600 23.96850 number of atom coordinates read : 3203 total number of charged atoms : 3053 net assigned charge : 0.9310091 assigned positive charge : 475.8069 centred at (gu) : 90.47068 89.47148 91.35258 assigned negative charge : -474.8770 centred at (gu) : 90.39115 89.52760 91.38718 start vw surface at 0.1300000 fill in re-entrant regions at 0.1400000 boundary points on vw surface= 7267 nv = 96 ne = 84 npr = 66073 no. pairs analyzed = 66073 no. exposed pairs = 3723 no. arc points = 25489 no. surface atoms = 1270 nbur = 1933 mkacc time = 0.1700000 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 = 1.484000 m= 343 mr = 4128 m= 1 mr = 22 m= 0 mr = 0 time to grow re-entrant surface = 0.2100000 no. cavity mid-points inaccessible to solvent = 29 time to turn everything in is 0.3600000 number of dielectric boundary points 3461 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2566 ## 260 charges are in solution ## iepsmp to db, and charging done at 0.4800000 number of grid points assigned charge 9225 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 9.6973740E-10 -1.1165666E-09 midg,1,midg; midg,igrid,midg 2.2422897E-09 -1.3013568E-09 1,midg,midg; igrid,midg,midg -1.9748367E-09 3.0045049E-09 gauss-seidel spectral radius is 0.9850969 estimated iterations to convergence 67 setup time was (sec) 0.6600000 now iterating at: 14:01:50 rms-change max change #iterations 0.1100324 16.10865 at 10iterations 9.2352731E-03 1.307930 at 20iterations 8.7761710E-04 0.1234150 at 30iterations 1.2551197E-04 2.1371841E-02 at 40iterations 2.8173934E-05 5.0888062E-03 at 50iterations finished qdiffx linear iterations at : 14:01:54 total time elapsed so far: 4.460000 # loops : 50 mean,max change (kT/e) : 2.8173934E-05 5.0888062E-03 energy calculations done at 4.460000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.620000 DelPhi exited at 14:01:55 4.626u 0.393s 0:05.71 87.7% 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 Mon Oct 10 2011 at 14:01:55 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3203 !!! WARNING: SEP 64 has a net charge of -0.4750 !!! WARNING: GLM 120 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 1.764910 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): -16.45200 34.17500 ymin,ymax (A): -1.758000 46.55000 zmin,zma (A): -6.288000 54.22500 x,y,z range (A): 50.62700 48.30800 60.51300 scale (grids/A): 1.764910 object centre (A): 8.861502 22.39600 23.96850 number of atom coordinates read : 3203 total number of charged atoms : 3053 net assigned charge : 0.9310091 assigned positive charge : 475.8069 centred at (gu) : 91.41106 88.41351 94.05682 assigned negative charge : -474.8770 centred at (gu) : 91.17308 88.58252 94.16127 start vw surface at 0.1200000 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 79209 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25489 grid for indexing accessible points = 1.400000 m= 28134 mr = 56251 m= 3839 mr = 20626 m= 122 mr = 2240 m= 1 mr = 9 m= 0 mr = 0 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 1103 time to turn everything in is 0.6200000 number of dielectric boundary points 32179 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 195 ## 1 charges are in solution ## iepsmp to db, and charging done at 0.7400000 number of grid points assigned charge 23772 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) : 0.5883033 object centre at (A) : 8.861502 22.39600 23.96850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.1805109E-02 -3.4430631E-02 midg,1,midg; midg,igrid,midg 7.7286079E-03 3.3243170E-03 1,midg,midg; igrid,midg,midg -1.0117737E-02 -2.6246437E-03 gauss-seidel spectral radius is 0.9984714 estimated iterations to convergence 203 setup time was (sec) 0.9200000 now iterating at: 14:01:56 rms-change max change #iterations 4.031723 160.9989 at 10iterations 1.798603 65.54331 at 20iterations 0.8059518 26.19843 at 30iterations 0.3624296 11.85091 at 40iterations 0.1620497 5.494982 at 50iterations 7.2901875E-02 2.658871 at 60iterations 3.2703899E-02 1.121254 at 70iterations 1.4727401E-02 0.4680824 at 80iterations 6.6170921E-03 0.2043161 at 90iterations 2.9907259E-03 9.5868111E-02 at 100iterations 1.3573454E-03 4.2429924E-02 at 110iterations 6.1990984E-04 2.2475481E-02 at 120iterations finished qdiffx linear iterations at : 14:02:06 total time elapsed so far: 10.36000 # loops : 120 mean,max change (kT/e) : 6.1990984E-04 2.2475481E-02 energy calculations done at 10.36000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 10.52000 DelPhi exited at 14:02:06 10.529u 0.455s 0:11.36 96.5% 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 Mon Oct 10 2011 at 14:02:06 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: 272 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3203 !!! WARNING: SEP 64 has a net charge of -0.4750 !!! WARNING: GLM 120 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= 7.0000000E-02 grid size : 179 scale,in grids/A, set to be: 2.647365 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): -16.45200 34.17500 ymin,ymax (A): -1.758000 46.55000 zmin,zma (A): -6.288000 54.22500 x,y,z range (A): 50.62700 48.30800 60.51300 scale (grids/A): 2.647365 object centre (A): 8.861502 22.39600 23.96850 number of atom coordinates read : 3203 total number of charged atoms : 3053 net assigned charge : 0.9310091 assigned positive charge : 475.8069 centred at (gu) : 92.11646 87.62005 96.08508 assigned negative charge : -474.8770 centred at (gu) : 91.75954 87.87368 96.24171 start vw surface at 0.1400000 fill in re-entrant regions at 0.5300000 boundary points on vw surface= 183750 reading accessible surface arcs data from file ARCDAT no. of arc points read = 25489 grid for indexing accessible points = 1.400000 m= 92661 mr = 136722 m= 31522 mr = 75706 m= 6622 mr = 25190 m= 541 mr = 4678 m= 11 mr = 253 m= 1 mr = 0 m= 0 mr = 0 time to grow re-entrant surface = 1.000000 no. cavity mid-points inaccessible to solvent = 3850 time to turn everything in is 1.640000 number of dielectric boundary points 72559 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.780000 number of grid points assigned charge 24422 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) : 1.764910 object centre at (A) : 8.861502 22.39600 23.96850 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.8641083 -0.7866059 midg,1,midg; midg,igrid,midg 3.4572158E-02 6.0006846E-02 1,midg,midg; igrid,midg,midg -0.1023135 -4.5818362E-02 gauss-seidel spectral radius is 0.9992215 estimated iterations to convergence 283 setup time was (sec) 1.970000 now iterating at: 14:02:09 rms-change max change #iterations 9.788555 292.6432 at 10iterations 5.605311 111.4224 at 20iterations 3.206167 66.15062 at 30iterations 1.827445 39.66883 at 40iterations 1.039640 20.39603 at 50iterations 0.5914575 10.71917 at 60iterations 0.3358677 6.368136 at 70iterations 0.1907900 3.466855 at 80iterations 0.1080984 2.075418 at 90iterations 6.1400231E-02 1.074459 at 100iterations 3.4869220E-02 0.6283131 at 110iterations 1.9773584E-02 0.4005065 at 120iterations 1.1217280E-02 0.2142582 at 130iterations 6.3900030E-03 0.1103840 at 140iterations 3.6571021E-03 6.8303585E-02 at 150iterations 2.1030863E-03 4.0924072E-02 at 160iterations 1.2225566E-03 2.3966312E-02 at 170iterations 7.2585669E-04 1.5794635E-02 at 180iterations finished qdiffx linear iterations at : 14:02:25 total time elapsed so far: 18.02000 # loops : 180 mean,max change (kT/e) : 7.2585669E-04 1.5794635E-02 energy calculations done at 18.02000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 18.19000 DelPhi exited at 14:02:25 18.196u 0.464s 0:19.05 97.9% 0+0k 0+0io 0pf+0w