Dear Guillaume,
Hi, I suggest you try the following changes:
amber on
watermodel tip4
LJcorrection on
rigidBonds water # Changed from "all"
useSettle on # Changed from "off"
rigidTolerance 1.0e-8 # Default, may need loosening to 1.0e-7 if
issues persist
Greeting,
Hector.
El 2026-03-06 05:18, Guillaume Petit via AMBER escribió:
> Dear Amber community,
> I have recently been trying to run simulations with NAMD, but using
> the more recent OPC/AMBER19sb forcefield combination (I am running
> protein - ligand simulations) prepared with Leap and Parmed from the
> Ambertool suit. From what I could find from online resources, this
> should be possible with NAMD 3 and above, using the following
> arguments in the configuration file:
> amber on
> watermodel tip4
> LJcorrection on
> rigidbonds all
> useSettle off
> and adjusting the 1-4 scaling.
> However when trying to run my system, I get some worrying warnings
> followed by crashes shortly after minimization:
> "Warning: Found 12713 H-H bonds."
> This is exactly the number of water molecules in my system, and I
> therefore assume that there is a problem with the way NAMD interprets
> the water in the topology file. After some digging, I found some old
> post suggesting building waters with:
> "set default flexiblewater on" flag in Leap as this should make some
> of the parameters more explicit for NAMD to read (even when
> subsequently running the simulation with rigid waters), but without
> success (still the same warning).
> I wonder if anyone else has come across similar issues and whether
> they were able to solve it (and importantly "how").
> I am relatively new to the world of MD and so, it is possible that I
> am missing something obvious (in which case I am happy to learn more).
> I can also supply more details/ files should that helps.
> Thank you for your help
> Best regards
> Guillaume
>
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--
--------------------------------------
Dr Hector A. Baldoni
Full Professor (FQByF - UNSL)
IMIBIO-SL - CONICET Researcher
Department of General and Inorganic Chemistry
National University of San Luis
Ejercito de los Andes 950 (D5700HHW)
San Luis - Argentina
hbaldoni at unsl dot edu dot ar
Tel.: +54-(0)266-4520300 ext. 6157
--------------------------------------
Por una Universidad Publica, Gratuita y Auditada.-
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Received on Fri Mar 06 2026 - 05:00:02 PST
