Dear Amber users
Atom number of a pdb [ 2nd column ] is not continuous
after using trim and reduce of AMBER command , instead " new" appears in
the last column. May I have to use some programs ( like perl ) to get
continuous as just before using the trim and reduce?
*Before* using " trim and then reduce" command of AMBER ( a portion of PDB)
ATOM 1 N MET A 0 2.087 8.287 -1.145 1.00
29.31 N
ATOM 2 CA MET A 0 1.516 9.645 -0.899 1.00
28.06 C
ATOM 3 C MET A 0 2.162 10.704 -1.788 1.00
27.19 C
ATOM 4 O MET A 0 1.619 11.752 -2.238 1.00
26.90 O
ATOM 5 CB MET A 0 1.819 9.901 0.601 1.00
31.06 C
ATOM 6 N LYS A 1 3.440 10.436 -2.034 1.00
24.33 N
ATOM 7 CA LYS A 1 4.326 11.276 -2.844 1.00
22.35 C
ATOM 8 C LYS A 1 5.166 10.393 -3.771 1.00
20.85 C
ATOM 9 O LYS A 1 5.580 9.289 -3.327 1.00
20.59 O
ATOM 10 CB LYS A 1 5.252 12.085 -1.921 1.00
22.60 C
ATOM 11 CG LYS A 1 4.400 13.116 -1.143 1.00
24.98 C
ATOM 12 CD LYS A 1 5.237 13.720 -0.049 1.00
27.59 C
ATOM 13 CE LYS A 1 4.283 14.413 0.937 1.00
29.67 C
ATOM 14 NZ LYS A 1 3.765 15.649 0.280 1.00
30.63 N
*After* using at first "trim" and then " reduce" command of AMBER ( a
portion of PDB)
ATOM 1 N MET A 0 2.087 8.287 -1.145 1.00
29.31 N
ATOM 2 CA MET A 0 1.516 9.645 -0.899 1.00
28.06 C
ATOM 3 C MET A 0 2.162 10.704 -1.788 1.00
27.19 C
ATOM 4 O MET A 0 1.619 11.752 -2.238 1.00
26.90 O
ATOM 5 CB MET A 0 1.819 9.901 0.601 1.00
31.06 C
ATOM 0 H1 MET A 0 1.458 7.592 -0.796 1.00
29.31 H new
ATOM 0 H2 MET A 0 2.220 8.154 -2.127 1.00
29.31 H new
ATOM 0 H3 MET A 0 2.967 8.205 -0.676 1.00
29.31 H new
ATOM 0 HA MET A 0 0.443 9.699 -1.134 1.00
28.06 H new
ATOM 6 N LYS A 1 3.440 10.436 -2.034 1.00
24.33 N
ATOM 7 CA LYS A 1 4.326 11.276 -2.844 1.00
22.35 C
Thanks ,
Mahendra Thapa
University of Cincinnati
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 13 2012 - 09:30:03 PDT
