It looks like the Amber 10 ambpdb creates a .pdb file that cannot be
read into tleap.
Specifically, using the same input files as the Amber 8 ambpdb the
atoms that were previously called H1,H2,H3 are called 1H,2H,2H.
Is this a bug, or is there something important that I'm overlooking?
Thank you,
-Sam
-Amber 8 output-
/extra/p530/software/amber8/exe/ambpdb
$ambpdb -p c141l.top < c141l.0.rst | head
| New format PARM file being parsed.
| Version = 1.000 Date = 12/07/06 Time = 13:42:51
REMARK
ATOM 1 N SER 1 56.880 -4.134 85.825
ATOM 2 H1 SER 1 56.272 -3.410 85.471
ATOM 3 H2 SER 1 56.406 -5.021 85.748
ATOM 4 H3 SER 1 57.709 -4.160 85.252
ATOM 5 CA SER 1 57.232 -3.861 87.241
ATOM 6 HA SER 1 56.390 -4.174 87.859
ATOM 7 CB SER 1 58.459 -4.673 87.684
ATOM 8 2HB SER 1 58.365 -5.703 87.334
ATOM 9 3HB SER 1 59.369 -4.241 87.262
-Amber 10 output-
$ambpdb -p c141l.top < c141l.0.rst | head
| New format PARM file being parsed.
| Version = 1.000 Date = 12/07/06 Time = 13:42:51
REMARK
ATOM 1 N SER 1 56.880 -4.134 85.825
ATOM 2 1H SER 1 56.272 -3.410 85.471
ATOM 3 2H SER 1 56.406 -5.021 85.748
ATOM 4 2H SER 1 57.709 -4.160 85.252
ATOM 5 CA SER 1 57.232 -3.861 87.241
ATOM 6 HA SER 1 56.390 -4.174 87.859
ATOM 7 CB SER 1 58.459 -4.673 87.684
ATOM 8 2HB SER 1 58.365 -5.703 87.334
ATOM 9 3HB SER 1 59.369 -4.241 87.262
--
Samuel A. Danziger
Dept. of Biomedical Engineering
PhD Candidate
University of California
Irvine, CA 92697
sdanzige.uci.edu
(908)246-4502
http://samdanziger.com/
Associated Graduate Students
VP Financial Affairs
vpfinance.ags.uci.edu
Truth Cannot Contradict Truth
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Received on Sun May 18 2008 - 06:08:14 PDT
