Re: QMMM param issue

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Apr 02 2020 - 03:30:27 CDT

Hi Marcelo
Although I understand that NAMD first checks the parameters, for the system
at issue I tried now QMMM with a smaller set of QM atoms around ligand YYY.
This includes only the nucleosides that were seen by X-ray diffr to
interact with a closely similar small ligand XXX, where no issue arose.
Five nucleosides, thus same charge -5, and no unpaired electron, in both
cases.
Same issue with YYY, the simulation crashing at

Info: SUMMARY OF PARAMETERS:
> Info: 810 BONDS
> Info: 2329 ANGLES
> Info: 5369 DIHEDRAL
> Info: 176 IMPROPER
> Info: 6 CROSSTERM
> Info: 321 VDW
> Info: 2 VDW_PAIRS
> Info: 0 NBTHOLE_PAIRS
> FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CG331 NG2R51 CG3RC1
> (ATOMS 3958 3967 3968)
> [Partition 0][Node 0] End of program
>

in contrast with the simulation with ligand XXX

Info: SUMMARY OF PARAMETERS:
> Info: 804 BONDS
> Info: 2310 ANGLES
> Info: 5320 DIHEDRAL
> Info: 176 IMPROPER
> Info: 6 CROSSTERM
> Info: 320 VDW
> Info: 2 VDW_PAIRS
> Info: 0 NBTHOLE_PAIRS
> Info: TIME FOR READING PSF FILE: 0.435593
> Info: Reading pdb file heat_restr50-01.pdb
> Info: TIME FOR READING PDB FILE: 0.0747963
> Info:
> Info: Using the following PDB file for QM parameters: sphere20-qm.pdb
> Info: Number of QM atoms (excluding Dummy atoms): 190
> Info: We found 8 QM-MM bonds.
> Info: Applying user defined multiplicity 1 to QM group ID 1
> Info: 1) Group ID: 1 ; Group size: 190 atoms ; Total PSF charge: -5
>

Does this suggest anything or is it just what should happen when NAMD has
problems with params?

All the best
francesco

On Thu, Apr 2, 2020 at 12:05 AM Marcelo C. R. Melo <melomcr_at_gmail.com>
wrote:

> 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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