From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Apr 03 2020 - 12:48:50 CDT
Hi Marcelo, Hi Josh
I set aside for the moment the above problem, going on with other ligands
of the same nucleosides. The new ligands, as before, only differ for a
substituent at the rings. I could run QMMM without problems for another two
systems, the third one gave again the problem of params:
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: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE CG2R_1
>
this time vdW, not angle.
Notice that NAMD had no problems in running MD with this system and same
.str parameter set.
Notice also that at the above crash point, NAMD had already read other
params, including those for the ligand. I can say that from warnings like
Warning: DUPLICATE vdW ENTRY FOR CG2R51
> PREVIOUS VALUES sigma=3.54578 epsilon=0.073 sigma14=3.54578
> epsilon14=0.073
> USING VALUES sigma=3.74177 epsilon=0.05 sigma14=3.74177 epsilon14=0.05
>
which relate to the ligand, and are the same as for the "good" cases
Notice, finally, that the .str parameter set has exactly the same layout in
all cases, the good ones and the bad ones.
Trying to pave the way to NAMD, I separated the .str into topology and
parameters, using the latter, Same issue.
What NAMD was looking for was present in .str and .prm in the form:
HT_W 0.000000 -0.046000 0.224500 ! TIP3P HYDROGEN PARAMETERS, adm
> jr., NBFIX obsolete
> OT_W 0.000000 -0.152100 1.768200 ! TIP3P OXYGEN PARAMETERS, adm
> jr., NBFIX obsolete
>
> CG3R_0 0.00 -0.0320 2.0000
> CG2D_0 0.00 -0.0680 2.0900
> CG2D_1 0.00 -0.0680 2.0900
> CG2R_0 0.00 -0.0730 1.9900
> CG2R_1 0.00 -0.0730 1.9900
> CG32_0 0.00 -0.0560 2.0100
>
> END
>
So, in my hands, NAMD_Git-2020-02-24_Linux-x86_64-multicore, either on my
home at the cluster or on my personal linux box, has scattered problems in
reading parameters when running QMMM, not when running MD.
Last year I carried out at the same cluster a large number of QMMM
simulations, using the same vmd ... prepare, for quite different systems
and with a previous version of NAMD (can't say which one, usually I use,
like now, nightbuilds). I never met the above problems of params.
The problem is so curious and baffling that I decided to set aside, from
now, the "bad" cases, working on the "good" ones (in all "good" cases
convergence gave no problems at a high DFT level). Perhaps I am missing
something. If so, it will emerge soon or later on rethinking. For now,
there is no point to change NAMD version.
Thanks for the kind advice that I received. I'll be back with new facts or
ideas on this problem of params, hopefully soon.
francesco
On Thu, Apr 2, 2020 at 6:41 PM Josh Vermaas <joshua.vermaas_at_gmail.com>
wrote:
> Hi Francesco,
>
> If NAMD can't find parameters, it'll bail. Looking back through the email
> chain, where in the parameter files that you passed *should* NAMD find the
> CG331 NG2R51 CG3RC1 parameters? They look like CGenFF atomtypes. Did you
> perhaps forget to pass the molecule to CGenFF or something else to provide
> dummy inputs? To be honest, if you are sure that the only place this angle
> occurs is in the QM region, I think its safe to just add a line to your
> parameter files like this to provide NAMD with something it can put in its
> memory banks:
>
> CG331 NG2R51 CG3RC1 0 0
>
> -Josh
>
> On Thu, Apr 2, 2020 at 3:20 AM Francesco Pietra <chiendarret_at_gmail.com>
> wrote:
>
>> 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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