From: Marcelo C. R. Melo (melomcr_at_gmail.com)
Date: Wed Apr 01 2020 - 17:05:32 CDT
Hi Francesco,
You did a thorough job testing this, so I'm running out of ideas.
Last thing that comes to mind is double checking the definition o the QM
region. NAMD removes the bonded interactions between QM atoms (to
avoid double counting the interactions already covered by the QM software),
but this happens *after* NAMD checks for parameters. Still, maybe there is
something being left out?
Let me know how this goes.
Best,
Marcelo
On Wed, 1 Apr 2020 at 17:16, Francesco Pietra <chiendarret_at_gmail.com> wrote:
> Hi Marcelo
> It is more than a puzzle for me.
>
> I restarted from the folder where minimization, heating, and NVT had been
> run for this system.
>
> I checked that NVT could be started again.
>
> Then, I built the files for qmmm (vmd ....prepare) into this folder with
> just the files that had served for NVT.
>
> Well, namd-01.conf (qmmm) gave the same error that I reported, while
> nvt-01.conf (classical MD) could be run again without problems.
>
> It is implied (but was also checked, and there are no voids in the .str)
> that the angle at issue is correctly defined.
>
> Yes, I had no problems with both MD and QMMM with other four very similar
> system, where the small molecule differs for only a substituent at a ring.
> Owing to that, I hope that I'll be able to think better tomorrow.
>
> All the best
> francesco
>
>
>
> On Wed, Apr 1, 2020 at 8:16 PM Marcelo C. R. Melo <melomcr_at_gmail.com>
> wrote:
>
>> Hi Francesco,
>>
>> It is curious that you have similar systems running without issue. Can I
>> guess that you created the parameters using CGenFF (or similar)?
>>
>> Maybe something in the topology definitions of this molecule is creating
>> an angle that doesn't have a parameter. Should this angle be defined at
>> all? It is hard to discuss without knowing more about the system, but maybe
>> something in the automatic topology creation got messed up.
>>
>> Best,
>> Marcelo
>>
>> On Wed, 1 Apr 2020 at 13:46, Francesco Pietra <chiendarret_at_gmail.com>
>> wrote:
>>
>>> I Marcelo
>>> I assumed that, providing all files from prepare, it will run, as it was
>>> the case on quite similar systems.
>>>
>>> The cluster was busy and it has only now tried to run the simulation
>>> with the same error message.
>>> Following your suggestion "some naming conflict for the atoms you
>>> mentioned (maybe double check the PSF file and the str file?)."
>>> I was unable to find any conflict for the atoms I mentioned. Here
>>> excerpts:
>>>
>>> .str file
>>> ATOM C5 CG3RC1 0.212
>>> ATOM C6 CG3C52 -0.073
>>> ATOM C7 CG3RC1 -0.138
>>> ATOM C8 CG3RC1 0.092
>>> ATOM C9 CG2D_0 0.434
>>> ATOM C10 CG2D_1 0.012
>>> ATOM C11 CG2R_0 -0.202
>>> ATOM C12 CG2R51 -0.235
>>> ATOM C13 CG2R51 -0.057
>>> ATOM N NG2R51 -0.021
>>> ATOM C15 CG331 -0.188
>>>
>>> *QMonly.psf file
>>> 324 MO4 640 ACL C5 CG3RC1 0.212000
>>> 12.0110 0
>>> 325 MO4 640 ACL C6 CG3C52 -0.073000
>>> 12.0110 0
>>> 326 MO4 640 ACL C7 CG3RC1 -0.138000
>>> 12.0110 0
>>> 327 MO4 640 ACL C8 CG3RC1 0.092000
>>> 12.0110 0
>>> 328 MO4 640 ACL C9 CG2D_0 0.434000
>>> 12.0110 0
>>> 329 MO4 640 ACL C10 CG2D_1 0.012000
>>> 12.0110 0
>>> 330 MO4 640 ACL C11 CG2R_0 -0.202000
>>> 12.0110 0
>>> 331 MO4 640 ACL C12 CG2R51 -0.235000
>>> 12.0110 0
>>> 332 MO4 640 ACL C13 CG2R51 -0.057000
>>> 12.0110 0
>>> 333 MO4 640 ACL N NG2R51 -0.021000
>>> 14.0070 0
>>> 334 MO4 640 ACL C15 CG331 -0.188000
>>> 12.0110
>>>
>>> general .psf file
>>> 3958 MO4 640 ACL C5 CG3RC1 0.212000
>>> 12.0110 0
>>> 3959 MO4 640 ACL C6 CG3C52 -0.073000
>>> 12.0110 0
>>> 3960 MO4 640 ACL C7 CG3RC1 -0.138000
>>> 12.0110 0
>>> 3961 MO4 640 ACL C8 CG3RC1 0.092000
>>> 12.0110 0
>>> 3962 MO4 640 ACL C9 CG2D_0 0.434000
>>> 12.0110 0
>>> 3963 MO4 640 ACL C10 CG2D_1 0.012000
>>> 12.0110 0
>>> 3964 MO4 640 ACL C11 CG2R_0 -0.202000
>>> 12.0110 0
>>> 3965 MO4 640 ACL C12 CG2R51 -0.235000
>>> 12.0110 0
>>> 3966 MO4 640 ACL C13 CG2R51 -0.057000
>>> 12.0110 0
>>> 3967 MO4 640 ACL N NG2R51 -0.021000
>>> 14.0070 0
>>> 3968 MO4 640 ACL C15 CG331 -0.188000
>>> 12.0110
>>>
>>> This isolated failure is so surprising to me that I would like to clear
>>> the matter. Do you have any other suggestion where i could check?
>>>
>>> thanks again
>>> francesco
>>>
>>>
>>> ---------- Forwarded message ---------
>>> From: Francesco Pietra <chiendarret_at_gmail.com>
>>> Date: Wed, Apr 1, 2020 at 6:09 PM
>>> Subject: Re: namd-l: QMMM param issue
>>> To: Marcelo C. R. Melo <melomcr_at_gmail.com>
>>> Cc: NAMD <namd-l_at_ks.uiuc.edu>
>>>
>>>
>>> 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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