Re: [AMBER] How to add the deprotonated SER residue to the ff14SB leap library?

From: David A Case <>
Date: Thu, 19 Oct 2017 12:06:36 -0400

On Thu, Oct 19, 2017, Michael Shokhen wrote:
> I couldn't find amber/dat/leap/lib/amino14.lib file in order to the
> above mentioned libraries comparison.

Yes: this is all so non-obvious...

If you look at the leaprc.protein.ff14SB file, you will notice that it
loads amino12.lib (and related N- and C-terminal residue files). This is
because what is now ff14SB went through a longish development phase, and there
was at one time an intermediate ff12SB version.

Since the only change from ff12SB to ff14SB was in parameters (and not in
anything that would be in the .lib file), we didn't update the library names,
to avoid breaking old behavior. But the upshot is the that library info for
ff14SB is actually in amino12.lib.

We should think about updating this for the next release. But if there is
ever uncertainty about exactly what is being used (for this purpose or
others), it's good to check about what is in the leaprc files that are being
loaded. (This is especially true for DNA and RNA, where naming schemes change
even more often than for proteins.)


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Received on Thu Oct 19 2017 - 09:30:04 PDT
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