Hi Tom,
Yes, the AMBER manual is definitely a fantastic resource and I also
agree that upon reading it carefully, the force field choice should be
clear. However, I do meet lots of people (mainly junior researchers)
that when asked what ff for nucleic acids they are using, they say
"ff99SB" or "ff14SB" ... And these are not isolated cases ....
Moreover, even in papers I reviewed I saw citations of Carlos's papers
for nucleic acids force fields.
And, yes, I do believe that the confusion comes from the naming of the
general purpose leaprc files .... For example, removing the "ff" and
"SB" from the names of the general leaprc files could help avoid the
confusion in my opinion .. The "ff" is usually connected to a force
field version, whereas a general purpose leaprc loads different force
field versions and modifications.
So, what I would suggest would be a general purpose leaprc named
"leaprc.14" or "leaprc.base.14" to replace the current "leaprc.ff14SB".
In addition, each modification could keep its own leaprc but I'd rename
those to use instead of the acronyms (e.g. ff14SB or chiOL3), the name
of the first author and the year of publication (or development if not
published) like "leaprc.proteins.Hornak.2006" or
"leaprc.RNA.[name].[year]" or "leaprc.DNA.[name].[year]" or
"leaprc.NA.[name].[year]" (if modification is for both DNA and RNA) and
so on.
The first lines of comments in the leaprc files could be extended a bit
with a brief history of the force fields that are loaded in that
particular leaprc.
I know this would need some work (as names of frcmod files would need to
be changed accordingly) but still I believe, this would be one way to
reduce in the future the confusion between leaprc file names and force
field versions. Moreover, the names of the files would also point to the
chronology of the modifications ...
Best wishes
Vlad
On 08/07/2015 03:31 AM, Thomas Cheatham wrote:
>> You are making exactly the confusion I was referring to .... "ff99SB" is
>> yet another protein-only force field .... I was not referring in any
>> line of my comment to this force field. Again, everything denoted with
>> "SB" are protein-only force fields ....
> While this may be true (the nomenclature ff14SB refers to the protein
> part), the "leaprc" file named leaprc.ff14SB contains both protein and
> nucleic acid parameters, as noted. Perhaps we should have named the
> default and recommended leaprc as of 2014:
>
> leaprc.ff14.recommended
>
> As noted, to understand what parameters are in a particular leaprc file,
> you have to read the manual and/or understand what is in the leaprc file
> (and also study the output from LEaP when building topologies).
>
> We have discussed separating out leaprc's for proteins vs. nucleic vs.
> lipid, etc and we admit that it can be very confusing with the current
> force field alphabet soup and many options available. However, the
> updated manuals in the current AmberTools do attempt to describe the force
> fields more clearly; if you have ideas how to improve further, we are
> happy to consider...
>
> --tec3
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Dr. Vlad Cojocaru
Computational Structural Biology Laboratory
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/43241/cojocaru
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Aug 07 2015 - 01:00:02 PDT
