RE: AMBER: Lone Pairs

From: Beale, John <>
Date: Tue, 13 Feb 2007 08:33:44 -0600

Thank you. Where can I access leaprc.ff02po1EP.r1? It doesn't appear to
be part of the AMBER 8.0 distribution.

John Beale
-----Original Message-----
From: [] On Behalf
Of David A. Case
Sent: Monday, February 12, 2007 3:25 PM
Subject: Re: AMBER: Lone Pairs

On Mon, Feb 12, 2007, Beale, John wrote:

> How are lone pairs handled in AMBER 8.0 (specifically in FF03)?

There are no lone pairs in FF03.

> I am
> trying to input a peptide into LEaP. The structure contains one
> methionine. The pdb file that I am loading was saved through SYBYL,
> two lone pairs are present in the pdb file, designated as "LPD". .
> I do a loadPdb in LEaP the program tells me that two lone pairs were
> added to the structure.

This makes sense: your pdb file has lone pairs in it, but the FF03
files don't know anything about lone pairs. Hence, LEaP thinks it needs
to "add" these to the structure. When the time comes to save a prmtop
file, LEaP should complain that it doesn't have enough information about
the lone-pairs to create a force field for them. (I'm guessing here:
you just said the "LEaP doesn't save the prmtop file", without any
indication of what the actual message is.)

There are some Amber force fields that include lone pairs (look for
leaprc files with "EP" in their filenames.) However, they are all quite
old, and are not really recommeded for any routine use. [Yong or Piotr
might want to chime in here: leaprc.ff02polEP.r1 is in fact "recent",
but I don't believe that it has been extensively tested.]

...good luck...dac
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Received on Wed Feb 14 2007 - 06:07:40 PST
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