That is strange. As you say, in LeAP the element type is listed as '?'.
In ff99SB they are 'H1' and the element type is 'H'. It seems from
frcmod.ff03 that H0 is the intended thing and all is well, just a minor
issue.
On Wed, Feb 15, 2012 at 4:31 AM, Dmitry Mukha <dvmukha.gmail.com> wrote:
> I have found something wrong in all_amino03.lib
>
> !entry.GLY.unit.atoms table str name str type int typex int resx int
> flags int seq int elmnt dbl chg
> "N" "N" 0 1 131072 1 7 -0.374282
> "H" "H" 0 1 131072 2 1 0.253981
> "CA" "CT" 0 1 131072 3 6 -0.128844
> * "HA2" "H0" 0 1 131072 4 -1 0.088859*
> * "HA3" "H0" 0 1 131072 5 -1 0.088859*
> "C" "C" 0 1 131072 6 6 0.580584
> "O" "O" 0 1 131072 7 8 -0.509157
>
> Element type for HA2 and HA3 for GLY is incorrect. It causes errors in some
> viewers when Amber trajectories are being reading.
>
> --
> Sincerely,
> Dmitry Mukha
> Institute of Bioorganic Chemistry, NAS, Minsk, Belarus
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>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Wed Feb 15 2012 - 06:00:02 PST
