Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber

From: David A Case <>
Date: Fri, 21 Aug 2020 22:06:09 -0400

On Fri, Aug 21, 2020, Charo del Genio wrote:

>Anyway, the first question is: the Amber20 manual talks about
>SIRAH, and even specifies where it should be found, i.e., in
>${AMBERHOME}/dat/SIRAH. However... it isn't there, and in fact it isn't
>even in the source tarball. Is it intended to be so?

That is a bug in preparing the distribution files. We'll get an update to
fix this. Thanks for the report.

>Second, upon downloading SIRAH and installing it in the above-mentioned
>location, leap dies with a buffer overflow when sourcing
>leaprc.sirah. The reason seems to be the presence of comment lines
>within LJoff.frcmod, in the SIRAH directory.

I can confirm the problem, but actual SIRAH users will have to chime in on
how they get around this.

[Matias: should we also have test cases in the Amber distribution? Scott:
would it be easy to skip comment lines (matching /^#/) in frcmod and
parameter files?]

This is Amber's first real foray into coarse-grained simulations, so there
may well be some rough edges. Thanks for helping out.


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Received on Fri Aug 21 2020 - 19:30:02 PDT
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