Re: [AMBER] Forcefield for RNA

From: <pavel.banas.upol.cz>
Date: Thu, 23 Oct 2014 22:54:28 +0200 (CEST)

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
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Received on Thu Oct 23 2014 - 14:00:02 PDT
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