From: Marcelo C. R. Melo (melomcr_at_gmail.com)
Date: Wed Apr 01 2020 - 09:57:44 CDT
NAMD check for available parameters for every system you try to load (QMMM
or not). Even if you have a QM region with no parameters, which will never
be simulated classically, you still need to provide NAMD with "dummy"
parameters to allow the simulation to start (QwikMD can help you create
dummy parameters for QM regions).
Therefore, this is likely an input problem. Either your NAMD config file is
not sourcing the right parameter file (*.str), or your str file has some
naming conflict for the atoms you mentioned (maybe double check the PSF
file and the str file?).
In fact, the names of the atom types in your str file suggest three carbon
atoms (CG3RC1 CG3C52 CG3RC1 ), while in your explanation you mention
two carbon and one nitrogen atoms (C5, N, C15), with different atom types,
but maybe that was a typo on your part (?).
On Wed, 1 Apr 2020 at 07:28, Francesco Pietra <chiendarret_at_gmail.com> wrote:
> With a QMMM (NAMD_Git-2020-02-24_Linux-x86_64-multicore on my home on the
> cluster) for a nucleic-smallmolecule system in TIP3, immediate crashwith
> UNABLE TO FIND ANGLE PARAMETERS FOR CG331 NG2R51 CG3RC1 (ATOMS 3958 C5,
> 3967 N, 3968 C15) [atom names added by myself]
> Actually, params for the requested angle are present in the .str file
> CG3RC1 CG3C52 CG3RC1 58.00 105.30
> This issue did not arise with minimizations and heating for the above
> system. I can also add that QMMM for a variety of similar systems,
> differing only slightly (and not for the atoms at issue) in the
> "smallmolecule" went on without any issue.
> The issue was reproduced on launching the simulation at the cluster from
> scratch and I fall short of realizing from where the issue can arise.
> Thanks for suggestions
> francesco pietra
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