Re: [AMBER] Forcefield for RNA

From: David A Case <>
Date: Thu, 23 Oct 2014 07:54:12 -0400

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.


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Received on Thu Oct 23 2014 - 05:00:02 PDT
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