Hi Vlad,
In nucleic12.lib, the RNA is denoted by G,A,C,U. The DNA is denoted by DA,
DT, DC, DG (and all 3' and 5' variants thereof).
This is a switch from older PDB versions where the RNA was denoted with RG
etc.
In nucleic12.lib the atom types are correct for applying the chi OL3 and
parmbsc0 changes (already incorporated into parm10.dat).
You shouldn't need to also load RNA_CI.lib.
Hope this helps,
Christina
On Tue, Oct 28, 2014 at 9:12 AM, Vlad Cojocaru <
vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> Dear all,
>
> We are now starting some simulations with the new force field
> recommendations as of AMBER14 ...
> In the manual it is written that the RNA force field included in ff14SB
> is ff99+bsc0+chiOL3 .... First, I also believe it is an unfortunate
> confusion to include nucleic acids force fields under the name "ff14SB"
> which is a protein force field.
>
> Second, I am confused because while the chiOL3 modifications are
> included in parm10.dat file, the nucleic12.lib library which is loaded
> in the leaprc.ff14SB file does not appear to contain any RNA units ....
> Is the "RNA_CI.lib", the correct RNA library to load ?
>
> Thanks a lot
>
> Best wishes
> Vlad
>
>
> On 10/23/2014 11:15 PM, Jiri Sponer wrote:
> > I have now noticed several papers telling
> > that either DNA or RNA has been simulated
> > with ff99SB, Hornak et al 2006. Basically,
> > it is impossible to tell which DNA or RNA force
> > field has been used, as no nucleic acid force field
> > is mentioned. Jiri
> >
> >
> >
> >
> > On Thu, 23 Oct 2014, pavel.banas.upol.cz wrote:
> >
> >> Date: Thu, 23 Oct 2014 22:54:28 +0200 (CEST)
> >> From: pavel.banas.upol.cz
> >> Reply-To: AMBER Mailing List <amber.ambermd.org>
> >> To: AMBER Mailing List <amber.ambermd.org>
> >> Subject: Re: [AMBER] Forcefield for RNA
> >>
> >> Dear all,
> >> the loading of force fields is indeed confusing when one is focused
> >> on non-
> >> protein systems. Contemporary generic force field is loaded by
> >> learrc.ff14
> >> SB, which is however labeled according to its protein part. Thus many
> >> users
> >> are confused and usually believe that SB correction is crucial for
> >> nucleic
> >> acids or at least it is worth to try. They do not even realize that is
> >> absolutely irrelevant for nucleic acids, while they should pay attention
> >> elsewhere.
> >>
> >> Possible solution would be to return back to the arrangement as it
> >> was for
> >> ff10, where force field was loaded as f10 that contained SB for
> >> proteins,
> >> bsc0 for DNA and bsc0+chiOL3 for RNA as a one simple but black-box
> >> package.
> >> Or alternatively split leaprc files to be system specific, so that
> >> user will
> >> have to choose proper force field variant for its particular system
> >> and in
> >> case of hybrid systems such as protein+DNA complexes to explicitely
> >> ask both
> >> for protein and DNA force fields. However, then the leap should complain
> >> when user will try to use e.g. protein force field for DNA.
> >>
> >> Pavel Banas
> >>
> >>
> >> --
> >> Pavel Banáš
> >> pavel.banas.upol.cz
> >> Department of Physical Chemistry,
> >> Palacky University Olomouc
> >> Czech Republic
> >>
> >>
> >>
> >> ---------- Původní zpráva ----------
> >> Od: David A Case <case.biomaps.rutgers.edu>
> >> Komu: AMBER Mailing List <amber.ambermd.org>
> >> Datum: 23. 10. 2014 13:55:31
> >> Předmět: Re: [AMBER] Forcefield for RNA
> >>
> >> "On Thu, Oct 23, 2014, Asfa Ali wrote:
> >>>
> >>> Also, as advised by Jiri Sponer, I didn't try chiOL3 along with
> >>> ff99bsc0.
> >>> If I have to do so, should I load both the force fields simultaneously?
> >>
> >> This is what you get by loading leaprc.ff14SB, as described in
> >> section 3.2.2
> >> of the Amber14 reference manual.
> >>
> >> Developers: this section far more confusing than it needs to be,
> >> and detailed instructions for Amber are very sparse. You don't find out
> >> until the final sentence what is in ff14SB for RNA, and I don't see any
> >> place that documents what is going on for DNA. The promised leaprc file
> >> for DNA has not yet been prepared. Table 3.1 marks ff99 as "current"
> >> (!?!?). We need explicit instructions on which leaprc (or other) files
> >> to load to get particular behavior. Basically, Section 3.2.2 has a good
> >> general overview of nucleic acid force fields, but too little in the way
> >> of specific information about Amber.
> >>
> >> ...dac
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber"
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >
> >
> > _______________________________________________
> > 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/research/teams/groups/rgcojocaru
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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Christina Bergonzo, PhD
Postdoctoral Researcher
Department of Medicinal Chemistry, University of Utah
30 South 2000 East, Rm. 201
Salt Lake City, UT 84112-5820
Office: L.S. Skaggs Pharmacy Research Institute, Rm.4290
http://home.chpc.utah.edu/~cheatham/
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Received on Tue Oct 28 2014 - 09:00:02 PDT
