Re: [AMBER] correct inconsistencies in [DR]NA_CI.lib

From: Jason Swails <>
Date: Tue, 6 Mar 2012 23:38:09 -0500

On Tue, Mar 6, 2012 at 11:57 AM, Thomas Gaillard <> wrote:

> Hi,
> The attached patch corrects what I believe could be (harmless)
> inconsistencies in DNA_CI.lib and RNA_CI.lib:
> - [DR][ACGTU]N residues are missing

Obviously if someone needed the free nucleotide, this would be an issue.

> - the "C5'" "CT" to "C5'" "CI" substitution is not applied in the
> atomspertinfo section

I'm not sure how urgent this is. Amber doesn't support perturbed topology
files with any program it has anymore (although I think tleap can still
write them).

> - sometimes the 131072 flag is changed to 131073

Neat! I'm pretty sure you can accomplish this by using the saveOFF command
in xleap after you've clicked on (thereby selecting) this atom. (That's
probably how these OFF files got that way in the first place). The only
effect this should have is that when you use the "edit" command for these
residues in xleap, any atom with the flag number 131073 should already be
selected in purple -- not a cause for concern.

Thanks for the report!

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Tue Mar 06 2012 - 21:00:02 PST
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