From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Apr 01 2020 - 11:09:29 CDT
Hi Marcelo
I should have transcribed the original
UNABLE TO FIND ANGLE PARAMETERS FOR CG331 NG2R51 CG3RC1 (ATOMS 3958 C5,
3967 N, 3968 C15)
Actually, that was a false message of error. The .str file was at the
cluster, while the problem arose from not having sent to the cluster all
files from the qmmm preparation (vmd -dispdev text -e prepare...tcl) on my
laptop.
Sorry for my lack of care. I should have better waited before posting, I
missed to follow the rule that one should rethink several times.
All the best
francesco
On Wed, Apr 1, 2020 at 4:58 PM Marcelo C. R. Melo <melomcr_at_gmail.com> wrote:
> Hi Francesco,
>
> 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 (?).
>
> Best,
> Marcelo
>
> On Wed, 1 Apr 2020 at 07:28, Francesco Pietra <chiendarret_at_gmail.com>
> wrote:
>
>> Hello
>> 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
>> error
>>
>> 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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