Re: [AMBER] Questions on force field

From: David A Case <>
Date: Fri, 13 Mar 2020 07:28:59 -0400

On Fri, Mar 13, 2020, Sasthi Mandal wrote:

> I have a doubt about nucleic acid force field. Are parmbsc0 and
>amberff99bsc0 same?

In the old days (5 years ago or so), Amber had "unified" leaprc files,
that loaded proteins, nucleic acids, water, and ions all together. So a
name like "amberff99bsc0" probably indicates some version of the "ff99"
protein force field (more likely to be ff99SB), and the bsc0 force field
for DNA. So the DNA part would be the same in the two systems you

You note that I said "probably" above, since I don't recognize the name
"amberff99bsc0", so cannot be sure what it entails. If you have the
actual leaprc files that are being used, you can see what is being
loaded by inspecting them.


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Received on Fri Mar 13 2020 - 04:30:02 PDT
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