From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Apr 01 2020 - 12:46:17 CDT
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
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
324 MO4 640 ACL C5 CG3RC1 0.212000
325 MO4 640 ACL C6 CG3C52 -0.073000
326 MO4 640 ACL C7 CG3RC1 -0.138000
327 MO4 640 ACL C8 CG3RC1 0.092000
328 MO4 640 ACL C9 CG2D_0 0.434000
329 MO4 640 ACL C10 CG2D_1 0.012000
330 MO4 640 ACL C11 CG2R_0 -0.202000
331 MO4 640 ACL C12 CG2R51 -0.235000
332 MO4 640 ACL C13 CG2R51 -0.057000
333 MO4 640 ACL N NG2R51 -0.021000
334 MO4 640 ACL C15 CG331 -0.188000
general .psf file
3958 MO4 640 ACL C5 CG3RC1 0.212000
3959 MO4 640 ACL C6 CG3C52 -0.073000
3960 MO4 640 ACL C7 CG3RC1 -0.138000
3961 MO4 640 ACL C8 CG3RC1 0.092000
3962 MO4 640 ACL C9 CG2D_0 0.434000
3963 MO4 640 ACL C10 CG2D_1 0.012000
3964 MO4 640 ACL C11 CG2R_0 -0.202000
3965 MO4 640 ACL C12 CG2R51 -0.235000
3966 MO4 640 ACL C13 CG2R51 -0.057000
3967 MO4 640 ACL N NG2R51 -0.021000
3968 MO4 640 ACL C15 CG331 -0.188000
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?
---------- 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>
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
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
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 (?).
> On Wed, 1 Apr 2020 at 07:28, Francesco Pietra <chiendarret_at_gmail.com>
>> 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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