On 6/6/25 6:30 AM, Pedro Martínez Zaragoza via AMBER wrote:
> [External Email]
>
> Dear AMBER developers and users,
> I have encountered an issue while running explicit solvent minimizations with positional restraints using AMBER24, following the standard protocol described in https://ambermd.org/tutorials/basic/tutorial13/index.php
> In my system, I apply positional restraints to all non-solvent atoms during the first minimization step:
>
> restraintmask = ':1-663',
> restraint_wt = 250.,
>
> Depending on the system, the number
> of residues can vary slightly (e.g., 662 or 663 for my protein alone,
> and up to 665–666 when including a Fe-OH cofactor and a substrate).
> Here is the problem:
>
> *
> Using AMBER24, the job fails silently (i.e., no output, crash before starting minimization cycles) when the mask includes: 1-663 or :1-666, even though these residues exist in the topology.
> *
> However, the exact same system, inputs, and mask work perfectly in AMBER22.
> *
> Curiously, AMBER24 only runs the minimization correctly when I use :1-662, even in systems that have 663–666 residues. This is unexpected and inconsistent with the behavior in AMBER22.
>
> The mdout
> file in AMBER24 doesn't show any clear error — just the standard
> startup information and then stops. Meanwhile, AMBER22 proceeds with the
> minimization and produces a full output, even if convergence is not
> achieved.
> This issue seems to be related to how restraintmask is parsed or applied in AMBER24, possibly in combination with how pmemd is handling restraint groups during minimization.
> Has anyone else experienced this? Could this be a regression or stricter parsing introduced in AMBER24?
> Any insights or suggestions are
> welcome. I’d be happy to provide topology and coordinate files if needed
> for reproducing the issue.
> Best regards,
>
> Pedro Martínez Zaragoza
>
> PhD Candidate – Computational Chemistry
>
> Universitat Autònoma de Barcelona
>
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--
Dr. Adrian E. Roitberg
Frank E. Harris Professor
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Fri Jun 06 2025 - 11:30:03 PDT
