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---- Dr. Charo I. del Genio Senior Lecturer in Statistical Physics Applied Mathematics Research Centre (AMRC) Design Hub Coventry University Technology Park Coventry CV1 5FB UK https://charodelgenio.weebly.com On Mon, 24 Aug 2020, 17:09 Matias Machado, <mmachado.pasteur.edu.uy> wrote: > Dear Charo, > > mmm... SIRAH failing on Linux that's something I've never seen... > > I'm a Linux-only user as well, and all SIRAH packages were tested OK on > different Linux DistrOS and HPC clusters... > > Can you please tell me more about your OS distribution and the AMBER > compilation? In particular, are you installing AMBER though conda? > > The LJoff issue I know is relate to the file format and Leap... but the > "buffer overflow" error is something new that I need to reproduce, > otherwise I can't tell you what's going on there... > > About your question: how do you know that the prmtop files obtained on a > machine that does not report the bug are correct? > > I never seen that to happen, not even in your case... one way or another > Leap fails generating the topology... the fact that you managed to > "overcame the error message" doesn't mean you haven't had an error in the > first place... > > Any way we will include some test cases during AMBER installation to check > for these issues... > > Jumping to the question of multiscaling... > > Simply mixing FG and CG is highly expected to fail... there are several > reasons for that, starting from incompatible interaction points, non-bonded > parameters at very different energy references and so on... so far we > provide some multiscale representations for DNA and solvent, but there's a > long way before getting to proteins... > > About the thermostats... > > If by "Bussi thermostat" you are referring to V-rescale, then it should > work, it's the one we use in GROMACS... Indeed I see no reason for any > thermostat to fail... > > All the best, > > Matias > > ----- Mensaje original ----- > De: "paraw" <the.paraw.gmail.com> > Para: "AMBER Mailing List" <amber.ambermd.org> > CC: "david case" <david.case.rutgers.edu> > Enviados: Lunes, 24 de Agosto 2020 12:19:42 > Asunto: [AMBER] Questions (and a small bug report) about SIRAH in Amber > > Dear Matias, > thank you very much for your reply. > As for the bug, I don't use MacOS. In fact, I only use Linux machines and > clusters (many of which I set up myself, in fact). Anyway, I'll wait for > more information about the workaround or a fix, but I wonder: how do you > know that the prmtop files obtained on a machine that does not report the > bug are correct? All you could say is that somehow the bug wasn't detected > or triggered there, and considering that we are talking about a buffer > overflow, the possibility of having overwritten some important memory > location cannot be excluded. > > Finally, I didn't CG the ligand. In one simulation, I just kept it FG, and > in another I simply got rid of it and added a network of harmonic > restraints to keep the shape of the active site. Note that the simulation > without ligand was unstable with the Bussi thermostat but stable if I first > eqiilibrated it with Langevin dynamics and gamma_ln=50, and then passed to > Bussi. The one with the ligand, instead, was only stable if I first heated > it extremely slowly (dt=0.001) at constant volume with Langevin thermostat, > before passing to constant pressure. > > So, my other questions remain: first, is SIRAH compatible with Bussi > thermostat, or does it need Langevin with high viscosity? Then, is the > strategy of leaving an atomistic ligand in a CG protein viable or not? > > > Thank you again, > > Charo > > > > > ---- > Dr. Charo I. del Genio > Senior Lecturer in Statistical Physics > > Applied Mathematics Research Centre (AMRC) > Design Hub > Coventry University Technology Park > Coventry CV1 5FB > UK > > https://charodelgenio.weebly.com > On Mon, 24 Aug 2020, 15:27 Matias Machado, <mmachado.pasteur.edu.uy> > wrote: > > > > 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 http://www.siraff.com) > > > > 3) THE FOLLOWING IS EXTREMELY IMPORTANT! > > 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... > > > > In any case DELETING THE FIRST LINES IN LJOFF ISN'T THE SOLUTION!!! > > 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, > > > > Matias > > > > ------------------------------------ > > PhD. > > Researcher at Biomolecular Simulations Lab. > > Institut Pasteur de Montevideo | Uruguay > > [http://pasteur.uy/en/labs/biomolecular-simulations-laboratory] > > [http://www.sirahff.com] > > > > ----- Mensaje original ----- > > De: "David A Case" <david.case.rutgers.edu> > > Para: "AMBER Mailing List" <amber.ambermd.org> > > CC: mmachado.pasteur.edu.uy > > 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. > > > > ...thx...dac > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Mon Aug 24 2020 - 10:00:02 PDT