Ahi Antti
I looked at your structures, but there were not output files.
Can you clarify what you mean by "blow-up" ?
Adrian
On 10/8/25 1:13 AM, Antti Salo via AMBER wrote:
> [External Email]
>
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Dr. Adrian E. Roitberg
Frank E. Harris Professor
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Oct 10 2025 - 09:00:03 PDT
