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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Received on Fri Mar 06 2026 - 00:30:02 PST
