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

From: Charo del Genio <the.paraw.gmail.com>
Date: Fri, 21 Aug 2020 21:43:18 +0100

Dear all,
        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?

Thank you,


Dr. Charo I. del Genio
Senior Lecturer in Statistical Physics
Applied Mathematics Research Centre (AMRC)
Design Hub
Coventry University Technology Park
Coventry CV1 5FB
AMBER mailing list
Received on Fri Aug 21 2020 - 14:00:03 PDT
Custom Search