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

From: Matias Machado <>
Date: Mon, 24 Aug 2020 11:26:57 -0300 (UYT)

Dear Charo,

Sorry for the delay answer, I'm recovering from a high fiver (luckily not COVID-19)... :-P

Any way, going to your questions:

1) As you point, SIRAH is not in ${AMBERHOME}/dat/SIRAH, I've just written to Sergio Pantano (the group leader) about the issue because I don't have the GitLab credentials to fix this at the AMBER's repo...

2) SIRAH is a stand alone package, so once downloaded it should work at any location as long as you correctly set the "addPath" command (check any AMBER tutorial at

We are aware of the bug you mention about "LJoff.frcmod"... so far we have only seen the issue in some MacOS, which may be your case... We are digging to fix it, I have some leads pointing either to the OS version (probably Catalina) or to the environment (perhaps Python)... but it's being hard to reproduce the error...

I'm witting in capitals because it seems to work (no error message is reported by leap), but no LJ corrections are applied!!!

So the generated prmtop is wrong and useless because SIRAH depends on those interactions to properly work. That explains the instabilities you see during the simulations.

There are some technical things about leap and the frcmod format, which I won't go into detail now, but the number of blank lines is important to properly read each section... I have a workaround but it needs more testing...

Hence, my STRONG advice at the moment is creating the topology files in Linux or in a MacOS that doesn't give any error.

4) Coarse-grainig ligands is difficult due to the many relevant interactions for binding. So far we don't have a systematic recipe to do it and it really depends on the case... So I have no idea how you managed to develop a compatible CG ligand for SIRAH...

All the best,


Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay

----- Mensaje original -----
De: "David A Case" <>
Para: "AMBER Mailing List" <>
Enviados: Viernes, 21 de Agosto 2020 23:06:09
Asunto: Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber

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.


AMBER mailing list
Received on Mon Aug 24 2020 - 07:30:04 PDT
Custom Search