Re: [AMBER] Possible bug in LEaP with ff12SB

From: Aronica, Pietro <>
Date: Thu, 25 Oct 2012 12:36:11 +0000

Alright, thanks.
From: [] on behalf of David A Case []
Sent: 25 October 2012 13:32
To: AMBER Mailing List
Subject: Re: [AMBER] Possible bug in LEaP with ff12SB

On Thu, Oct 25, 2012, Aronica, Pietro wrote:

> > set UNIT.1.3 element C

You syntax is wrong here: as the error message says, the final entry must be a
string. When LEaP sees a bare set of letters, it tries to find out if it
corresponds to an object; if none is found it identifies it is a string.

But the command really should be this:

set UNIT.1.3 element "C"

To be sure, there are lots of examples in the LEaP manual that don't have the
quotation marks, and just happen to work because there was no object that
matched the unquoted string. But we can't change the name of cytosine--that's
determined by IUPAC and the PDB. The correct way is write all strings with
quotes. I'm going through the AmberTools Reference Manual to try to fix all
the examples.

[As an aside: this has nothing to do with ff12SB per se: it has to do with
the PDB change in residue nomenclature from version 2 to version 3 of the
PDB format. ff12SB (and ff10 before it) just happen to be some of the
first sets of library files to use the new nomenclature.]

...good luck....dac

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