Tue Oct 11 01:43:26 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 Tue Oct 11 2011 at 01:43:26 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2753 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 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= 9.0000004E-02 grid size : 179 scale,in grids/A, set to be: 0.6258460 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): 10.03200 62.77900 ymin,ymax (A): -56.14200 0.7410000 zmin,zma (A): -35.28300 7.531000 x,y,z range (A): 52.74700 56.88300 42.81400 scale (grids/A): 0.6258460 object centre (A): 36.40550 -27.70050 -13.87600 number of atom coordinates read : 2753 total number of charged atoms : 2601 net assigned charge : 4.312014 assigned positive charge : 416.2066 centred at (gu) : 89.50923 88.99489 90.08903 assigned negative charge : -411.8952 centred at (gu) : 89.55444 89.25610 89.87199 start vw surface at 0.2000000 fill in re-entrant regions at 0.2100000 boundary points on vw surface= 7105 nv = 96 ne = 84 npr = 56148 no. pairs analyzed = 56148 no. exposed pairs = 3277 no. arc points = 22926 no. surface atoms = 1106 nbur = 1647 mkacc time = 0.1600000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 314 mr = 3993 m= 1 mr = 34 m= 0 mr = 0 time to grow re-entrant surface = 0.1800000 no. cavity mid-points inaccessible to solvent = 110 time to turn everything in is 0.4000000 number of dielectric boundary points 3393 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2253 ## 218 charges are in solution ## iepsmp to db, and charging done at 0.5400000 number of grid points assigned charge 8634 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid -1.4355789E-08 2.2017950E-08 midg,1,midg; midg,igrid,midg 3.1352130E-08 -1.4792193E-08 1,midg,midg; igrid,midg,midg 8.5239993E-09 1.2669085E-10 gauss-seidel spectral radius is 0.9867861 estimated iterations to convergence 71 setup time was (sec) 0.6700000 now iterating at: 01:43:27 rms-change max change #iterations 0.1386267 20.72828 at 10iterations 1.3689741E-02 1.790207 at 20iterations 1.7557198E-03 0.3341827 at 30iterations 3.9442186E-04 8.9401245E-02 at 40iterations 1.0582005E-04 2.5344849E-02 at 50iterations finished qdiffx linear iterations at : 01:43:30 total time elapsed so far: 3.800000 # loops : 50 mean,max change (kT/e) : 1.0582005E-04 2.5344849E-02 energy calculations done at 3.800000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 4.050000 DelPhi exited at 01:43:31 4.052u 0.171s 0:04.89 86.2% 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 Tue Oct 11 2011 at 01:43:31 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2753 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 1.877538 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): 10.03200 62.77900 ymin,ymax (A): -56.14200 0.7410000 zmin,zma (A): -35.28300 7.531000 x,y,z range (A): 52.74700 56.88300 42.81400 scale (grids/A): 1.877538 object centre (A): 36.40550 -27.70050 -13.87600 number of atom coordinates read : 2753 total number of charged atoms : 2601 net assigned charge : 4.312014 assigned positive charge : 416.2066 centred at (gu) : 88.52714 86.98421 90.26660 assigned negative charge : -411.8952 centred at (gu) : 88.66279 87.76794 89.61562 start vw surface at 0.2100000 fill in re-entrant regions at 0.3500000 boundary points on vw surface= 77651 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22926 grid for indexing accessible points = 1.400000 m= 27568 mr = 54738 m= 4124 mr = 20585 m= 153 mr = 2704 m= 0 mr = 33 time to grow re-entrant surface = 0.3300000 no. cavity mid-points inaccessible to solvent = 2882 time to turn everything in is 0.7300000 number of dielectric boundary points 31436 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 175 iepsmp to db, and charging done at 0.8900000 number of grid points assigned charge 20441 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) : 0.6258460 object centre at (A) : 36.40550 -27.70050 -13.87600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -6.8776095E-03 3.5414029E-02 midg,1,midg; midg,igrid,midg 2.2789525E-02 -3.7054561E-02 1,midg,midg; igrid,midg,midg 6.1065680E-04 8.6483900E-03 gauss-seidel spectral radius is 0.9986074 estimated iterations to convergence 212 setup time was (sec) 1.100000 now iterating at: 01:43:33 rms-change max change #iterations 4.292832 184.1390 at 10iterations 1.982772 65.55991 at 20iterations 0.9195148 32.37302 at 30iterations 0.4292809 13.46025 at 40iterations 0.1986830 6.840578 at 50iterations 9.2565730E-02 3.163877 at 60iterations 4.3386217E-02 1.508601 at 70iterations 2.0237444E-02 0.6208076 at 80iterations 9.5277512E-03 0.2948732 at 90iterations 4.5481622E-03 0.1481304 at 100iterations 2.2241515E-03 7.9086304E-02 at 110iterations 1.1286916E-03 4.2545319E-02 at 120iterations finished qdiffx linear iterations at : 01:43:41 total time elapsed so far: 9.320000 # loops : 120 mean,max change (kT/e) : 1.1286916E-03 4.2545319E-02 energy calculations done at 9.320000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 9.560000 DelPhi exited at 01:43:41 9.560u 0.225s 0:10.18 96.0% 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 Oct 11 2011 at 01:43:41 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: 306 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2753 !!! WARNING: GLM 262 has a net charge of -0.0940 !!! WARNING: GLM 266 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= 0.1000000 grid size : 179 scale,in grids/A, set to be: 2.816307 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): 10.03200 62.77900 ymin,ymax (A): -56.14200 0.7410000 zmin,zma (A): -35.28300 7.531000 x,y,z range (A): 52.74700 56.88300 42.81400 scale (grids/A): 2.816307 object centre (A): 36.40550 -27.70050 -13.87600 number of atom coordinates read : 2753 total number of charged atoms : 2601 net assigned charge : 4.312014 assigned positive charge : 416.2066 centred at (gu) : 87.79047 85.47620 90.39970 assigned negative charge : -411.8952 centred at (gu) : 87.99412 86.65187 89.42328 start vw surface at 0.2000000 fill in re-entrant regions at 0.6100000 boundary points on vw surface= 179704 reading accessible surface arcs data from file ARCDAT no. of arc points read = 22926 grid for indexing accessible points = 1.400000 m= 90347 mr = 132492 m= 31825 mr = 74586 m= 7385 mr = 25913 m= 855 mr = 5718 m= 28 mr = 529 m= 0 mr = 13 time to grow re-entrant surface = 1.050000 no. cavity mid-points inaccessible to solvent = 9933 time to turn everything in is 1.790000 number of dielectric boundary points 70893 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 3 iepsmp to db, and charging done at 1.960000 number of grid points assigned charge 20808 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) : 1.877538 object centre at (A) : 36.40550 -27.70050 -13.87600 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid -3.8854726E-02 0.3572374 midg,1,midg; midg,igrid,midg -8.9515209E-02 -0.5106799 1,midg,midg; igrid,midg,midg -1.4346265E-02 5.7771467E-02 gauss-seidel spectral radius is 0.9992493 estimated iterations to convergence 288 setup time was (sec) 2.180000 now iterating at: 01:43:44 rms-change max change #iterations 9.997931 294.5739 at 10iterations 5.775401 119.9017 at 20iterations 3.317168 62.19067 at 30iterations 1.904407 34.39767 at 40iterations 1.091695 20.65835 at 50iterations 0.6248334 11.32774 at 60iterations 0.3576054 6.757347 at 70iterations 0.2045457 3.633350 at 80iterations 0.1172883 1.969519 at 90iterations 6.7225948E-02 1.145741 at 100iterations 3.8439665E-02 0.7554359 at 110iterations 2.2066206E-02 0.4037561 at 120iterations 1.2721950E-02 0.2663651 at 130iterations 7.3795780E-03 0.1503487 at 140iterations 4.3299762E-03 8.6688995E-02 at 150iterations 2.5970503E-03 5.8563232E-02 at 160iterations 1.6099570E-03 3.8478851E-02 at 170iterations 1.0508249E-03 2.6428223E-02 at 180iterations finished qdiffx linear iterations at : 01:43:57 total time elapsed so far: 15.23000 # loops : 180 mean,max change (kT/e) : 1.0508249E-03 2.6428223E-02 energy calculations done at 15.23000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 15.46000 DelPhi exited at 01:43:58 15.460u 0.253s 0:16.12 97.4% 0+0k 0+0io 0pf+0w