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

From: Michael Shokhen <>
Date: Mon, 23 Oct 2017 13:51:58 +0000

Dear David and other Amber experts who tried to help
with the reported problem,

Thank you for your advises and sorry for my delayed response.
I have been trying many variants and finally got to the point.
The solution was to follow the amber tutorial B5.
The initial command of the tutorial uses antechamber in order to convert
input file in CIF format with non-standard residue to the ac file format.
Unfortunately, I couldn’t find any way how to convert initial PDB format of
my non-standard residue to the requested CIF format.
Working the problem around I used a two steps file conversion:
PDB to mol2 and then mol2 to ac.
Following the remaining B5 protocol I have generated the correct topology for the
deprotonated SER and incorporated it into the protein.


From: David A Case <>
Sent: Thursday, October 19, 2017 7:06:36 PM
To: AMBER Mailing List
Subject: Re: [AMBER] How to add the deprotonated SER residue to the ff14SB leap library?

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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