Tue Nov 22 14:10:17 PST 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 Nov 22 2011 at 14:10:22 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1948 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 0.6021243 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): 8.747001 48.85600 ymin,ymax (A): -15.38300 26.33400 zmin,zma (A): -11.34300 47.78100 x,y,z range (A): 40.10900 41.71700 59.12400 scale (grids/A): 0.6021243 object centre (A): 28.80150 5.475500 18.21900 number of atom coordinates read : 1948 total number of charged atoms : 1816 net assigned charge : 3.000004 assigned positive charge : 284.1981 centred at (gu) : 91.15944 90.30505 89.86993 assigned negative charge : -281.1983 centred at (gu) : 91.26296 90.40679 89.86843 start vw surface at 7.0000000E-02 fill in re-entrant regions at 7.9999998E-02 boundary points on vw surface= 4628 nv = 96 ne = 84 npr = 40898 no. pairs analyzed = 40898 no. exposed pairs = 2411 no. arc points = 16934 no. surface atoms = 830 nbur = 1118 mkacc time = 7.0000008E-02 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 202 mr = 2436 m= 1 mr = 26 m= 0 mr = 0 time to grow re-entrant surface = 7.9999998E-02 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.1600000 number of dielectric boundary points 2369 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1722 ## 192 charges are in solution ## iepsmp to db, and charging done at 0.2400000 number of grid points assigned charge 5720 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.4241585E-09 1.4276029E-09 midg,1,midg; midg,igrid,midg 3.9772790E-09 -1.5889455E-09 1,midg,midg; igrid,midg,midg 3.3202034E-09 -2.0243685E-09 gauss-seidel spectral radius is 0.9856665 estimated iterations to convergence 68 setup time was (sec) 0.4000000 now iterating at: 14:10:25 rms-change max change #iterations 9.3088873E-02 14.88933 at 10iterations 8.0995681E-03 1.620140 at 20iterations 6.6535769E-04 0.1168594 at 30iterations 5.7848589E-05 9.2163086E-03 at 40iterations 4.9057762E-06 9.7012520E-04 at 50iterations finished qdiffx linear iterations at : 14:10:36 total time elapsed so far: 3.890000 # loops : 50 mean,max change (kT/e) : 4.9057762E-06 9.7012520E-04 energy calculations done at 3.890000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.020000 DelPhi exited at 14:10:38 4.027u 0.231s 0:16.59 25.6% 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 Nov 22 2011 at 14:10:40 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1948 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 1.806373 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): 8.747001 48.85600 ymin,ymax (A): -15.38300 26.33400 zmin,zma (A): -11.34300 47.78100 x,y,z range (A): 40.10900 41.71700 59.12400 scale (grids/A): 1.806373 object centre (A): 28.80150 5.475500 18.21900 number of atom coordinates read : 1948 total number of charged atoms : 1816 net assigned charge : 3.000004 assigned positive charge : 284.1981 centred at (gu) : 93.47839 90.91514 89.60987 assigned negative charge : -281.1983 centred at (gu) : 93.78905 91.22061 89.60537 start vw surface at 7.9999998E-02 fill in re-entrant regions at 0.1300000 boundary points on vw surface= 49745 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16934 grid for indexing accessible points = 1.400000 m= 16804 mr = 33494 m= 2236 mr = 12216 m= 93 mr = 1319 m= 0 mr = 35 time to grow re-entrant surface = 0.1200000 no. cavity mid-points inaccessible to solvent = 95 time to turn everything in is 0.2700000 number of dielectric boundary points 21814 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 156 iepsmp to db, and charging done at 0.3700000 number of grid points assigned charge 14187 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) : 0.6021243 object centre at (A) : 28.80150 5.475500 18.21900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.9475342E-02 2.5205616E-02 midg,1,midg; midg,igrid,midg 7.8957761E-03 -2.4083357E-04 1,midg,midg; igrid,midg,midg 4.8170672E-03 -1.6243036E-03 gauss-seidel spectral radius is 0.9984006 estimated iterations to convergence 198 setup time was (sec) 0.5400000 now iterating at: 14:10:45 rms-change max change #iterations 3.166293 136.3825 at 10iterations 1.390738 59.61469 at 20iterations 0.6119941 24.81137 at 30iterations 0.2694283 11.33975 at 40iterations 0.1190083 4.876145 at 50iterations 5.2135795E-02 1.885458 at 60iterations 2.2919036E-02 0.8578434 at 70iterations 1.0059426E-02 0.3446698 at 80iterations 4.4266288E-03 0.1708813 at 90iterations 1.9430213E-03 8.0257893E-02 at 100iterations 8.5067522E-04 3.1024933E-02 at 110iterations 3.7574480E-04 1.6305923E-02 at 120iterations finished qdiffx linear iterations at : 14:11:09 total time elapsed so far: 8.750000 # loops : 120 mean,max change (kT/e) : 3.7574480E-04 1.6305923E-02 energy calculations done at 8.750000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 8.890000 DelPhi exited at 14:11:11 8.895u 0.280s 0:31.43 29.1% 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 Tue Nov 22 2011 at 14:11:13 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: 228 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 1948 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 2.9999999E-02 grid size : 179 scale,in grids/A, set to be: 2.709559 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): 8.747001 48.85600 ymin,ymax (A): -15.38300 26.33400 zmin,zma (A): -11.34300 47.78100 x,y,z range (A): 40.10900 41.71700 59.12400 scale (grids/A): 2.709559 object centre (A): 28.80150 5.475500 18.21900 number of atom coordinates read : 1948 total number of charged atoms : 1816 net assigned charge : 3.000004 assigned positive charge : 284.1981 centred at (gu) : 95.21755 91.37269 89.41480 assigned negative charge : -281.1983 centred at (gu) : 95.68371 91.83095 89.40820 start vw surface at 7.0000000E-02 fill in re-entrant regions at 0.2500000 boundary points on vw surface= 114985 reading accessible surface arcs data from file ARCDAT no. of arc points read = 16934 grid for indexing accessible points = 1.400000 m= 55549 mr = 81107 m= 18606 mr = 45160 m= 3728 mr = 14850 m= 437 mr = 2709 m= 18 mr = 287 m= 0 mr = 4 time to grow re-entrant surface = 0.3600000 no. cavity mid-points inaccessible to solvent = 342 time to turn everything in is 0.6700000 number of dielectric boundary points 49206 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 4 iepsmp to db, and charging done at 0.7800000 number of grid points assigned charge 14522 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) : 1.806373 object centre at (A) : 28.80150 5.475500 18.21900 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.2696639 0.2422507 midg,1,midg; midg,igrid,midg 6.0913231E-02 2.9572356E-02 1,midg,midg; igrid,midg,midg 2.9380074E-02 1.1871774E-02 gauss-seidel spectral radius is 0.9991738 estimated iterations to convergence 275 setup time was (sec) 0.9700000 now iterating at: 14:11:19 rms-change max change #iterations 7.682774 370.3515 at 10iterations 4.330068 119.9460 at 20iterations 2.426263 56.44164 at 30iterations 1.352202 35.49828 at 40iterations 0.7539905 18.20171 at 50iterations 0.4195432 8.952965 at 60iterations 0.2329206 5.292206 at 70iterations 0.1294937 2.807335 at 80iterations 7.2022438E-02 1.627502 at 90iterations 3.9929375E-02 0.9511375 at 100iterations 2.2163039E-02 0.4794970 at 110iterations 1.2317642E-02 0.2516544 at 120iterations 6.8495288E-03 0.1414185 at 130iterations 3.8027754E-03 7.7556610E-02 at 140iterations 2.1148017E-03 4.5015335E-02 at 150iterations 1.1730264E-03 2.8190136E-02 at 160iterations 6.5034069E-04 1.3455391E-02 at 170iterations 3.6250387E-04 7.7021122E-03 at 180iterations finished qdiffx linear iterations at : 14:11:59 total time elapsed so far: 14.32000 # loops : 180 mean,max change (kT/e) : 3.6250387E-04 7.7021122E-03 energy calculations done at 14.32000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 14.43000 DelPhi exited at 14:12:02 14.434u 0.298s 0:48.92 30.0% 0+0k 0+0io 0pf+0w