Re: [AMBER-Developers] [AMBER] ATTN GLYCAM users: CY atom type work around

From: case <>
Date: Sat, 10 Dec 2011 09:24:11 -0500

On Sat, Dec 10, 2011, Jodi Ann Hadden wrote:

> Currently there is an issue with the CY atom type which overlaps in
> ff99SB and GLYCAM.

Thanks for looking into this. Note that ff10 and ff11r4 also have some
new atom types for proteins. Can you check for additional name overlaps.
(You need to switch the "ff11" branch to get ff11 parameters.)

> - Go to and download the most up-to-date version
> of the parameters.

It looks like Glycam_06g-1.dat is slightly different from the corresonding
file (GLYCAM-06g.dat) in the git repo. Can you bring the latter up to
date, probably putting the full id in the header line, removing references
to "Amber 8" etc.

> - If you are building a system that contains a carbohydrate, load
> GLYCAM, ff99SB, then GLYCAM again.
> source leaprc.GLYCAM_06
> source leaprc.ff99SB
> source leaprc.GLYCAM_06

Can you explain why this works? Is there a fix going forward that eliminates
the need for this workaround?


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Received on Sat Dec 10 2011 - 06:30:03 PST
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