Hello!
I've been preparing structures for AMBER MD simulations using ff19SB forcefield and the OPC water model, as suggested in the manual.
My system stays intact during minimization steps, but blows up already during the first step of system relaxation and creating vacuums.
I have a GDP ligand and a Mg2+ -ion in the systems.
I have gone through the files looking for some reason behind this, but still cannot understand what is wrong.
In leap.log, I noticed a note after loading the OPC water model with "source leaprc.water.opc":
"""
Parameters for OPC water (JPCL, 2014, 5 (21), pp 3863-3871)
(UNKNOWN ATOM TYPE: EP)
"""
Is this something that I should be worried about or not? I've seen the same note in some previous posts here, but those haven't been answered.
The minimization and equilibration (relaxation) I've been using are working for other structures of my colleagues, so those are most likely not the problem.
I have attached the fundamental files (and some pictures of the systems) as a funet filesender link.
https://filesender.funet.fi/?s=download&token=7789d389-ee2f-466b-b96c-a16274234d9c
-Antti
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Received on Wed Oct 08 2025 - 01:30:02 PDT
