Sun Oct 9 16:18:41 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 16:18:41 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3062 !!! WARNING: GLM 164 has a net charge of -0.0940 !!! WARNING: GLM 233 has a net charge of -0.0940 !!! WARNING: MG3 345 has a net charge of 1.4000 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: 0.6285977 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): -14.98200 37.40500 ymin,ymax (A): 54.07200 107.0030 zmin,zma (A): -3.673000 52.96100 x,y,z range (A): 52.38700 52.93100 56.63400 scale (grids/A): 0.6285977 object centre (A): 11.21150 80.53750 24.64400 number of atom coordinates read : 3062 total number of charged atoms : 2910 net assigned charge : -3.287975 assigned positive charge : 452.1791 centred at (gu) : 90.27257 88.82400 91.38287 assigned negative charge : -455.4685 centred at (gu) : 90.30365 88.69860 91.42704 start vw surface at 0.1700000 fill in re-entrant regions at 0.1800000 boundary points on vw surface= 7986 nv = 96 ne = 84 npr = 63097 no. pairs analyzed = 63097 no. exposed pairs = 3750 no. arc points = 26255 no. surface atoms = 1278 nbur = 1784 mkacc time = 0.1500000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 478 mr = 4384 m= 3 mr = 52 m= 0 mr = 0 time to grow re-entrant surface = 0.1700000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 4031 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2606 ## 225 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 9861 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 8.4604324E-10 -1.0251021E-08 midg,1,midg; midg,igrid,midg -2.0496454E-08 7.0076567E-09 1,midg,midg; igrid,midg,midg -9.3522003E-11 -6.6464017E-09 gauss-seidel spectral radius is 0.9869318 estimated iterations to convergence 72 setup time was (sec) 0.5900000 now iterating at: 16:18:41 rms-change max change #iterations 0.1489301 20.62923 at 10iterations 1.4151484E-02 2.002622 at 20iterations 1.3772406E-03 0.2153246 at 30iterations 1.7049712E-04 2.6051521E-02 at 40iterations 4.9793001E-05 9.6549988E-03 at 50iterations finished qdiffx linear iterations at : 16:18:44 total time elapsed so far: 3.220000 # loops : 50 mean,max change (kT/e) : 4.9793001E-05 9.6549988E-03 energy calculations done at 3.220000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.410000 DelPhi exited at 16:18:45 3.418u 0.149s 0:04.09 86.7% 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 Sun Oct 9 2011 at 16:18:45 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3062 !!! WARNING: GLM 164 has a net charge of -0.0940 !!! WARNING: GLM 233 has a net charge of -0.0940 !!! WARNING: MG3 345 has a net charge of 1.4000 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: 1.885793 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): -14.98200 37.40500 ymin,ymax (A): 54.07200 107.0030 zmin,zma (A): -3.673000 52.96100 x,y,z range (A): 52.38700 52.93100 56.63400 scale (grids/A): 1.885793 object centre (A): 11.21150 80.53750 24.64400 number of atom coordinates read : 3062 total number of charged atoms : 2910 net assigned charge : -3.287975 assigned positive charge : 452.1791 centred at (gu) : 90.81676 86.47110 94.14788 assigned negative charge : -455.4685 centred at (gu) : 90.91080 86.09543 94.28094 start vw surface at 0.1600000 fill in re-entrant regions at 0.2900000 boundary points on vw surface= 86586 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26255 grid for indexing accessible points = 1.400000 m= 31186 mr = 60145 m= 5220 mr = 22485 m= 316 mr = 3213 m= 7 mr = 115 m= 0 mr = 0 time to grow re-entrant surface = 0.3100000 no. cavity mid-points inaccessible to solvent = 718 time to turn everything in is 0.6400000 number of dielectric boundary points 37357 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 159 iepsmp to db, and charging done at 0.7600000 number of grid points assigned charge 22865 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) : 0.6285977 object centre at (A) : 11.21150 80.53750 24.64400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 2.0010551E-02 6.0629616E-03 midg,1,midg; midg,igrid,midg -3.0204421E-02 -9.4228145E-03 1,midg,midg; igrid,midg,midg -2.6932964E-02 -2.3689911E-02 gauss-seidel spectral radius is 0.9986495 estimated iterations to convergence 216 setup time was (sec) 0.9200000 now iterating at: 16:18:46 rms-change max change #iterations 4.557313 171.0334 at 10iterations 2.131781 71.39932 at 20iterations 1.002040 29.53524 at 30iterations 0.4693683 14.43081 at 40iterations 0.2208512 7.121789 at 50iterations 0.1038950 3.229258 at 60iterations 4.8821211E-02 1.508768 at 70iterations 2.2943035E-02 0.6625900 at 80iterations 1.0808568E-02 0.3725414 at 90iterations 5.0876681E-03 0.1534891 at 100iterations 2.4118165E-03 6.9668293E-02 at 110iterations 1.1519308E-03 3.4395218E-02 at 120iterations finished qdiffx linear iterations at : 16:18:52 total time elapsed so far: 7.420000 # loops : 120 mean,max change (kT/e) : 1.1519308E-03 3.4395218E-02 energy calculations done at 7.420000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 7.610000 DelPhi exited at 16:18:53 7.608u 0.196s 0:08.34 93.4% 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 16:18:53 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: 271 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 3062 !!! WARNING: GLM 164 has a net charge of -0.0940 !!! WARNING: GLM 233 has a net charge of -0.0940 !!! WARNING: MG3 345 has a net charge of 1.4000 atomic coordinates, charges and radii written to file fort.19 time to read in and/or assign rad/chrg= 7.9999998E-02 grid size : 179 scale,in grids/A, set to be: 2.828690 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): -14.98200 37.40500 ymin,ymax (A): 54.07200 107.0030 zmin,zma (A): -3.673000 52.96100 x,y,z range (A): 52.38700 52.93100 56.63400 scale (grids/A): 2.828690 object centre (A): 11.21150 80.53750 24.64400 number of atom coordinates read : 3062 total number of charged atoms : 2910 net assigned charge : -3.287975 assigned positive charge : 452.1791 centred at (gu) : 91.22496 84.70639 96.22179 assigned negative charge : -455.4685 centred at (gu) : 91.36613 84.14310 96.42127 start vw surface at 0.1500000 fill in re-entrant regions at 0.5200000 boundary points on vw surface= 200656 reading accessible surface arcs data from file ARCDAT no. of arc points read = 26255 grid for indexing accessible points = 1.400000 m= 100109 mr = 146414 m= 36945 mr = 80994 m= 9489 mr = 29244 m= 1400 mr = 7020 m= 89 mr = 913 m= 1 mr = 41 m= 0 mr = 0 time to grow re-entrant surface = 0.9700000 no. cavity mid-points inaccessible to solvent = 2254 time to turn everything in is 1.610000 number of dielectric boundary points 84063 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.750000 number of grid points assigned charge 23278 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) : 1.885793 object centre at (A) : 11.21150 80.53750 24.64400 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.3652858 0.1488367 midg,1,midg; midg,igrid,midg -0.3122261 -0.2467832 1,midg,midg; igrid,midg,midg -0.3956845 -0.2824529 gauss-seidel spectral radius is 0.9992747 estimated iterations to convergence 293 setup time was (sec) 1.920000 now iterating at: 16:18:55 rms-change max change #iterations 10.77807 337.5974 at 10iterations 6.355529 132.0916 at 20iterations 3.715749 71.87211 at 30iterations 2.168077 41.79218 at 40iterations 1.264660 22.39361 at 50iterations 0.7342756 13.01884 at 60iterations 0.4271806 8.129001 at 70iterations 0.2477293 4.609413 at 80iterations 0.1435701 2.749320 at 90iterations 8.3333775E-02 1.642019 at 100iterations 4.8204049E-02 0.9692755 at 110iterations 2.7962960E-02 0.4533157 at 120iterations 1.6173307E-02 0.2804489 at 130iterations 9.3543865E-03 0.1564789 at 140iterations 5.4194783E-03 9.4394684E-02 at 150iterations 3.1387853E-03 5.5322647E-02 at 160iterations 1.8195288E-03 3.0717850E-02 at 170iterations 1.0593089E-03 2.0599365E-02 at 180iterations finished qdiffx linear iterations at : 16:19:06 total time elapsed so far: 12.34000 # loops : 180 mean,max change (kT/e) : 1.0593089E-03 2.0599365E-02 energy calculations done at 12.34000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 12.53000 DelPhi exited at 16:19:06 12.533u 0.181s 0:12.98 97.9% 0+0k 0+0io 0pf+0w