Dear Amber community,
I have recently been trying to run simulations with NAMD, using the more recent OPC/AMBER19sb forcefield combination (I am looking at protein - ligand interactions) prepared with Leap and ParmEd from the Ambertool suit (2024). 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 topology (waters show up as O H1 H2 EPW, mass and charge of each atoms seems correct to me) . After some digging, I found some old post suggesting building water with:
“set default flexiblewater on” flag in Leap as this should make some of the parameters more explicit for NAMD to read, but without success as I get the same warnings. Of note, the system runs fine with pmemd.
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 missed something obvious (in which case I would be happy to learn). I can supply more details and files as required to help with narrowing down the problem.
Thank you for your help
Best regards
Guillaume
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Received on Wed Dec 24 2025 - 01:00:02 PST
