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

From: Scott Brozell <>
Date: Fri, 21 Aug 2020 21:21:46 -0400


On Fri, Aug 21, 2020 at 09:43:18PM +0100, Charo del Genio wrote:
> I have a few question and a bug to report concerning SIRAH in Amber. I am not sure whether the bug is more properly in leap o in the SIRAH files, so I'm CCing Matias Machado onto this email.
> 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?
> 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. In fact, the problem disappears upon removing all such lines except the very first one (the title line). As I mentioned before, I don't know whether this
> is a bug in leap or whether the frcmod file is not supposed to have comment lines except the title one. Anyway, the workaround is easy.
> Finally, what is perhaps the actually interesting question: can SIRAH deal with organic ligands? I ask because if I try to simulate a coarse-grained protein with a bound ligand, I am completely unable
> to have any stability. In the very first few steps after minimization everything just falls apart with vlimit exceeded every step. Conversely, if I remove the ligand, the simulation proceeds seemingly
> without problems. Note that the FG simulation of protein with ligand has no problems.
> On a related note, I also found that if I use the Bussi thermostat, I end up with a similar situation, namely the protein falling apart, regardless of the presence of a ligand. However, the simulation
> is stable if using a Langevin thermostat with a huge gamma_ln constant of 50. Is that normal behaviour for the CG field?

I confirm that ${AMBERHOME}/dat/SIRAH isn't in my
473704 -rw-rw---- 1 amber 483165473 May 12 17:27 AmberTools20.tar.bz2
This is likely an oversight that we'll correct soon.

addpath /amber/dat/SIRAH
source leaprc.sirah

Works for me. Note this:
Some machines have a very
restrictive policy on allocating available resources:
increase the datasize, stacksize, and memoryuse
using the limit, ulimit, or unlimit commands;
for many Linuxes this command sequence will work:
limit; unlimit; limit
Otherwise read the man pages or apply trial and error
to find the apt use of these commands.

I do not know.

Thanks for the report.

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Received on Fri Aug 21 2020 - 18:30:02 PDT
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