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From: Marinus Veldhuizen (Mac.Veldhuizen_at_uantwerpen.be)
Date: Wed Oct 02 2024 - 03:15:05 CDT
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Dear VMD community member,
Thank you for making time to read this email. I am currently working on calculating the partial atomic charges for the ONOH molecule using the Force Field Toolkit (FFTK) in VMD and have encountered some challenges. The initial partial charges obtained with the standard settings appear unrealistic for both cis and trans conformation. However, after adjusting the "Water Shift - End" setting under the "Advanced" tab, and increasing it to 3.0 (from the default value of 0.4), I observed that the partial charges are going towards a more sensible value.
Although the partial charges look more sensible now, given that the final partial charge should be somewhere between the charges of the two conformations, I am a bit wary when doing parameterization. Therefore, I was wondering if changing the distance of the water this much is sensible. Hence, I have the following questions you can hopefully shed some light on.
*
Is the initial charge (with the standard settings) unrealistic because there is a mismatch between the QM data and the MM data? Because by changing the distance a better solution can be found for ΔU MM-QM to Δd MM-QM [1]? And therefore the solution is no longer found at ΔU = Δd = 0?
([1] Introduction to Force Field Toolkit - Christopher Mayne / youtube around 14:30 )
* Would increasing the water shift distance significantly cause the QM-calculated input data for the charge calculated to be not applicable anymore? (Because the QM data is calculated at a much shorter distance)
*
Could it be that the issue of the partial charges arises because it is an acid (pKa = 3,398)?
*
Because of the influence of water on the acid, FFTK has difficulty to assessing the polarization (μMM-μQM)?
*
Lastly, if the water shift is not an option, do you have any advice on how to proceed?
I tried searching in the literature but could not find an explanation. Additionally, I could not find an email which had a similar issue. Therefore, hopefully, you can give me some input. Sorry for the long mail.
Kind regards,
Mac
P.S. Here is some additional information
For the trans conformation, the partial charges were calculated as:
standard settings O: -0.996 - N: 0.995, O: -0.413, H: 0.414
increased "Water Shift - End" O: -0.229 - N: 0.194, O: -0.398, H: 0.433
while for the cis conformation, the values were:
standard settings O: -0.924, N: 0.083, O: -0.134, H: 1.000
increased "Water Shift - End" O: -0.505, N: 0.378, O: -0.689, H: 0.816
This might not be of use but I have tried the following:
Doubled checked the geometry.
Set All z-coordinates of all atoms to 0 (perfectly planar molecule).
Increased initial water positions by 50%/100% (pre-QM calculations).
Compute the esp charges (using Gaussian) to see if there is something wrong. It shows that the influence of water does not cause abnormal esp charges.
Different versions of VMD, 1.9.3 and 1.9.4a57
I use Gaussian 16
I have parameterized other molecules successfully, so I do not think there is something wrong with my VMD. Finally, I tried to add the files of the computation but that is not allowed?
- Next message: Nakshatra Upadhyay: "Two different type of color set for potential map of overlapped molecules"
- Previous message: Roni Saiba: "Re: VMD 1.9.4 NAMDEnergy plugin query"
- Next in thread: Marinus Veldhuizen: "Re: FFTK partial charge assignment weak acid ONOH (HNO2) - Water Shift settings"
- Reply: Marinus Veldhuizen: "Re: FFTK partial charge assignment weak acid ONOH (HNO2) - Water Shift settings"
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