VMD-L Mailing List

From: Per Larsson (larsson.r.per_at_gmail.com)
Date: Wed Sep 25 2019 - 02:21:09 CDT

Hi JC,

Thanks for your input. This is also a good suggestion, and something that I also actually did. The resulting parameterization generally has very low penalties (zero in many cases, especially the fatty acid moiety). In fact, there is only one dihedral with a penalty score above 10, and three or four charges with penalties around 15.

But I am not sure how to proceed from here with ffTK. I do find the ”start from cgenff” tab, and can read in my resulting str-file. If you don’t mind me asking a few basic methodological questions then. For optimization of charges, do I only calculate water interactions for those atoms with a high charge penalty? Charge groups or not, the total charge on my molecule is either -1 (as the ionized species) or 0, so I need the sum of charges to sum to that. Do I include all the low-penalty charges as constraints somehow? Similar question also for the dihedral, do I specifically only scan that dihedral and optimize against QM-data?

Thanks for your patience
/Per

> 23 sep. 2019 kl. 00:04 skrev Gumbart, JC <gumbart_at_physics.gatech.edu>:
>
> Good advice from Josh, as always. We go a step further by first running the molecule through CGenFF: https://cgenff.umaryland.edu/ <https://cgenff.umaryland.edu/>
> and only then parametrizing those regions with high penalties. No need to reinvent the wheel for common moieties already present in the FF.
>
> Best,
> JC
>
>> On Sep 20, 2019, at 5:31 AM, Per Larsson <larsson.r.per_at_gmail.com <mailto:larsson.r.per_at_gmail.com>> wrote:
>>
>> Hi Josh,
>>
>> Many thanks for your reply. All of what you are saying makes sense. I will start by adding a shorter fatty acid chain as you suggest to the dihedral incorporated. Let me work on this some more and I’ll report back any additional problems (or success).
>>
>> Thanks
>> /Per
>>
>>
>>
>>> 19 sep. 2019 kl. 18:50 skrev Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov <mailto:Joshua.Vermaas_at_nrel.gov>>:
>>>
>>> Hi Per,
>>>
>>> I think atom groups are useful to think about here, even though fftk doesn't believe they exist. Basically, each CH2 group in your fatty acid alone will be charge neutral. The ester or whatever other linkage will also be close to charge neutral. So whatever charge is on the deleted atoms (hopefully just a hydrogen?) would get added onto the attachment point. For systems I've worked with before, this tends to be a carbon, which will have a charge very close to 0 in the final result.
>>>
>>> To get around the unparameterized bonds, angles and dihedrals, how bad would it be to cut the fatty acid down to an ethyl or propyl group? In that case, you would definitely assign fixed 0.09, -0.18 and -0.27 to the hydrogens and carbons, but you'd be able to explicitly scan the dihedrals you'd be missing.
>>>
>>> -Josh
>>>
>>>
>>> On 2019-09-19 06:16:35-06:00 owner-vmd-l_at_ks.uiuc.edu <mailto:owner-vmd-l_at_ks.uiuc.edu> wrote:
>>>
>>> Hi all,
>>>
>>> I am trying to use the ffTK to parameterize a rather large (41 atoms) molecule, which consists of a salicylamide part and a hydro-carbon chain ending with a carbonyl group (so essentially a fatty acid) bound to the nitrogen of the salicylamide.
>>> Aside from being quite large, so the QM calculations take quite some time, I also have issues with placing the water molecules properly for determination of interactions energies, presumably due to steric clashes with nearby atoms.
>>>
>>> I did submit the molecule to Paramchem, and the high penalties (43 at most for a dihedral, 16 for the charges) are all found in the salicylamide part of the molecule. Therefore I think it makes sense to split the ffTK parameterization, working on the salicylamide and essentially leaving the fatty acid tail as it is.
>>> However, what then becomes the strategy for eventually joining these two fragments at the end? If I do get optimized charges for example, those will then sum to zero, right, but when I add in the fatty acid part, the total sum is not going to be zero again, most likely? Do I include this by saying that the hydrogen atom which is lost upon joining the fragments should bear the full charge sum of the fatty acid tail? And how about bonds, angles, dihedrals that cross between these two fragments?
>>>
>>> Many thanks in advance
>>> /Per
>>>
>>>
>>>
>>
>