AFAIK for files lacking an explicit element column, a CA justified in
the manner that Miranda pointed out in tleap should be interpreted as
a calcium, not a carbon -- so this should be fixed if possible.
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
http://www.cgl.ucsf.edu
On Aug 2, 2010, at 11:46 AM, Yi Shang wrote:
> Dear all,
> I noticed that CX atom type in ff10 (CA atoms) got printed out as
> "CA "
> instead of " CA " (different in spacing) in pdb file generated by
> AMBER11
> tleap. Was it changed on purpose? It doesn't seem to be consistent
> with PDB
> standard format.
>
> Since ff10 is not an official release yet, and most programs (like
> tleap)
> are not sensitive to spacing in atom name, this post may be trivial.
> But in
> the future for other programs that use fixed width to read in PDB
> format
> files, spacing may cause problems.
>
> Here is a section of the pdb file I got.
> =============================================================
> ATOM 17 N GLN 2 16.076 13.799 28.506 1.00 0.00
> ATOM 18 H GLN 2 15.940 12.817 28.377 1.00 0.00
> ATOM 19 CA GLN 2 17.389 14.278 28.102 1.00 0.00
> ATOM 20 HA GLN 2 17.529 15.324 28.412 1.00 0.00
> ATOM 21 CB GLN 2 18.500 13.474 28.767 1.00 0.00
> ATOM 22 HB2 GLN 2 18.402 13.565 29.859 1.00 0.00
> ATOM 23 HB3 GLN 2 18.368 12.410 28.520 1.00 0.00
> ATOM 24 CG GLN 2 19.904 13.906 28.358 1.00 0.00
> ATOM 25 HG2 GLN 2 20.075 13.638 27.305 1.00 0.00
> ATOM 26 HG3 GLN 2 19.983 15.001 28.428 1.00 0.00
> ATOM 27 CD GLN 2 20.976 13.269 29.219 1.00 0.00
> ATOM 28 OE1 GLN 2 21.166 13.646 30.379 1.00 0.00
> ATOM 29 NE2 GLN 2 21.681 12.291 28.657 1.00 0.00
> ATOM 30 HE21 GLN 2 22.409 11.830 29.184 1.00 0.00
> ATOM 31 HE22 GLN 2 21.485 12.014 27.706 1.00 0.00
> ATOM 32 C GLN 2 17.460 14.142 26.591 1.00 0.00
> ATOM 33 O GLN 2 17.139 13.089 26.042 1.00 0.00
> ===============================================================
>
> Thank you!
>
> --
> Yi (Miranda) Shang
> PhD candidate
> Graduate Program in Molecular and Cellular Biology
> Stony Brook University
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Mon Aug 02 2010 - 13:30:03 PDT
