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
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Received on Mon Aug 02 2010 - 12:00:06 PDT
