Tue Oct 11 07:51:27 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 07:51:27 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2389 !!! WARNING: HIQ 45 has a net charge of 0.5140 !!! WARNING: HIR 93 has a net charge of 0.5140 !!! WARNING: SEP 192 has a net charge of -0.4750 !!! WARNING: GLM 194 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 0.6380386 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): -8.797000 36.58300 ymin,ymax (A): -14.82400 40.97200 zmin,zma (A): 5.365000 52.35700 x,y,z range (A): 45.38000 55.79600 46.99200 scale (grids/A): 0.6380386 object centre (A): 13.89300 13.07400 28.86100 number of atom coordinates read : 2389 total number of charged atoms : 2247 net assigned charge : 3.959008 assigned positive charge : 361.2953 centred at (gu) : 90.42105 88.68330 90.65179 assigned negative charge : -357.3368 centred at (gu) : 90.34303 88.68899 90.81020 start vw surface at 0.2300000 fill in re-entrant regions at 0.2400000 boundary points on vw surface= 6480 nv = 96 ne = 84 npr = 48211 no. pairs analyzed = 48211 no. exposed pairs = 2848 no. arc points = 20049 no. surface atoms = 977 nbur = 1412 mkacc time = 0.1000000 writing accessible surface arcs data to file ARCDAT grid for indexing accessible points = 1.400000 m= 350 mr = 3598 m= 1 mr = 55 m= 0 mr = 0 time to grow re-entrant surface = 0.1100000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.3600000 number of dielectric boundary points 3178 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 2035 ## 219 charges are in solution ## iepsmp to db, and charging done at 0.4700000 number of grid points assigned charge 7769 setting boundary conditions some initial phi values: midg,midg,1; midg,midg,igrid 1.8549169E-08 -1.2569627E-08 midg,1,midg; midg,igrid,midg 8.0456282E-09 3.7791157E-09 1,midg,midg; igrid,midg,midg -2.2267281E-09 1.4646787E-08 gauss-seidel spectral radius is 0.9872535 estimated iterations to convergence 72 setup time was (sec) 0.5900000 now iterating at: 07:51:28 rms-change max change #iterations 0.1422273 20.90785 at 10iterations 1.4620686E-02 2.264752 at 20iterations 1.6765250E-03 0.2845993 at 30iterations 2.6385995E-04 3.9218903E-02 at 40iterations 5.4106462E-05 8.8348389E-03 at 50iterations finished qdiffx linear iterations at : 07:51:31 total time elapsed so far: 3.330000 # loops : 50 mean,max change (kT/e) : 5.4106462E-05 8.8348389E-03 energy calculations done at 3.330000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 3.540000 DelPhi exited at 07:51:32 3.539u 0.154s 0:04.60 80.0% 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 07:51:32 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2389 !!! WARNING: HIQ 45 has a net charge of 0.5140 !!! WARNING: HIR 93 has a net charge of 0.5140 !!! WARNING: SEP 192 has a net charge of -0.4750 !!! WARNING: GLM 194 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= 0.1200000 grid size : 179 scale,in grids/A, set to be: 1.914116 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): -8.797000 36.58300 ymin,ymax (A): -14.82400 40.97200 zmin,zma (A): 5.365000 52.35700 x,y,z range (A): 45.38000 55.79600 46.99200 scale (grids/A): 1.914116 object centre (A): 13.89300 13.07400 28.86100 number of atom coordinates read : 2389 total number of charged atoms : 2247 net assigned charge : 3.959008 assigned positive charge : 361.2953 centred at (gu) : 91.26263 86.04967 91.95528 assigned negative charge : -357.3368 centred at (gu) : 91.02897 86.06685 92.43045 start vw surface at 0.2100000 fill in re-entrant regions at 0.3000000 boundary points on vw surface= 69422 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20049 grid for indexing accessible points = 1.400000 m= 26908 mr = 48375 m= 4411 mr = 20362 m= 267 mr = 2849 m= 3 mr = 93 m= 0 mr = 2 time to grow re-entrant surface = 0.2300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 0.5600000 number of dielectric boundary points 29330 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 140 iepsmp to db, and charging done at 0.6700000 number of grid points assigned charge 17675 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) : 0.6380386 object centre at (A) : 13.89300 13.07400 28.86100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 3.6583930E-02 -2.5379634E-02 midg,1,midg; midg,igrid,midg 8.0156792E-03 3.1011578E-02 1,midg,midg; igrid,midg,midg -3.0606908E-03 5.1213317E-03 gauss-seidel spectral radius is 0.9986258 estimated iterations to convergence 214 setup time was (sec) 0.8200000 now iterating at: 07:51:33 rms-change max change #iterations 4.122561 188.5600 at 10iterations 1.927574 71.83871 at 20iterations 0.9072242 32.12371 at 30iterations 0.4237510 13.30286 at 40iterations 0.1984344 6.389027 at 50iterations 9.3201801E-02 2.903595 at 60iterations 4.3649200E-02 1.360321 at 70iterations 2.0509887E-02 0.7075481 at 80iterations 9.6668769E-03 0.2990799 at 90iterations 4.5485701E-03 0.1537399 at 100iterations 2.1832068E-03 7.3898315E-02 at 110iterations 1.0544873E-03 3.2462120E-02 at 120iterations finished qdiffx linear iterations at : 07:51:39 total time elapsed so far: 6.780000 # loops : 120 mean,max change (kT/e) : 1.0544873E-03 3.2462120E-02 energy calculations done at 6.780000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 6.970000 DelPhi exited at 07:51:40 6.968u 0.210s 0:08.17 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 Tue Oct 11 2011 at 07:51:40 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: 328 assigning charges and radii... opening formatted file:fort.13 number of atoms read in = 2389 !!! WARNING: HIQ 45 has a net charge of 0.5140 !!! WARNING: HIR 93 has a net charge of 0.5140 !!! WARNING: SEP 192 has a net charge of -0.4750 !!! WARNING: GLM 194 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: 2.871173 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): -8.797000 36.58300 ymin,ymax (A): -14.82400 40.97200 zmin,zma (A): 5.365000 52.35700 x,y,z range (A): 45.38000 55.79600 46.99200 scale (grids/A): 2.871173 object centre (A): 13.89300 13.07400 28.86100 number of atom coordinates read : 2389 total number of charged atoms : 2247 net assigned charge : 3.959008 assigned positive charge : 361.2953 centred at (gu) : 91.89389 84.07452 92.93288 assigned negative charge : -357.3368 centred at (gu) : 91.54342 84.10023 93.64552 start vw surface at 0.1600000 fill in re-entrant regions at 0.4300000 boundary points on vw surface= 160216 reading accessible surface arcs data from file ARCDAT no. of arc points read = 20049 grid for indexing accessible points = 1.400000 m= 85077 mr = 116811 m= 33098 mr = 70463 m= 8020 mr = 27160 m= 1088 mr = 6185 m= 74 mr = 722 m= 0 mr = 25 time to grow re-entrant surface = 0.7300000 no. cavity mid-points inaccessible to solvent = 0 time to turn everything in is 1.260000 number of dielectric boundary points 66207 no. dielectric boundary points in salt = 0 no. grid points charged and at boundary= 1 iepsmp to db, and charging done at 1.380000 number of grid points assigned charge 17967 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) : 1.914116 object centre at (A) : 13.89300 13.07400 28.86100 pulling boundary values out of old potential map... some initial phi values: midg,midg,1; midg,midg,igrid 0.4159088 -0.3491226 midg,1,midg; midg,igrid,midg -0.1213365 0.3172777 1,midg,midg; igrid,midg,midg -1.4641101E-02 -3.3872895E-02 gauss-seidel spectral radius is 0.9992484 estimated iterations to convergence 288 setup time was (sec) 1.530000 now iterating at: 07:51:42 rms-change max change #iterations 9.633823 461.0753 at 10iterations 5.611671 132.1842 at 20iterations 3.254512 74.99551 at 30iterations 1.881121 39.94115 at 40iterations 1.084980 21.22217 at 50iterations 0.6233441 13.30971 at 60iterations 0.3583342 6.829136 at 70iterations 0.2057622 4.015373 at 80iterations 0.1180199 2.229084 at 90iterations 6.7736186E-02 1.282575 at 100iterations 3.8860045E-02 0.7652168 at 110iterations 2.2294419E-02 0.3912411 at 120iterations 1.2826145E-02 0.2505989 at 130iterations 7.3679355E-03 0.1345203 at 140iterations 4.2546238E-03 9.2681885E-02 at 150iterations 2.4823844E-03 4.4544220E-02 at 160iterations 1.4668315E-03 2.8522491E-02 at 170iterations 8.8500121E-04 1.7471313E-02 at 180iterations finished qdiffx linear iterations at : 07:51:51 total time elapsed so far: 10.87000 # loops : 180 mean,max change (kT/e) : 8.8500121E-04 1.7471313E-02 energy calculations done at 10.87000 writing potential map in DELPHI format potential map written to file fort.14 total cpu time was (sec) 11.04000 DelPhi exited at 07:51:53 11.042u 0.178s 0:12.62 88.8% 0+0k 0+0io 0pf+0w