[gmx-users] grompp error : Atomtype CAro not found

[Justin Lemkul]

On 3/3/20 2:47 AM, Atila Petrosian wrote:
> Dear Justin and Dallas,
>
> Thanks for your answers. I am so confused. I am beginner in MD simulation
> of lipid + small molecule.
>
> '' There are far better options for lipids than the old Berger parameters
> used in the tutorial. I wrote the tutorial in 2008 and it reflected a
> common protocol at the time ''.
> Justin, please suggest me better parameter for lipids, exactly (point out
> the web site).

I suggest you spend some time investigating the literature as many 
comparison studies have been done. This is a critical choice that you 
must make in designing your simulation study. The force field you choose 
needs to adequately cover all the elements of your system, not just the 
lipids.

> '' Since you are using ATB to generate the topology for your small
> molecule, then it stands to reason that you then should use ATB for the
> lipid molecule. '' Dallas, are you sure ATB can be used for lipids ???

Here I disagree with Dallas. Any robust force field already supports 
lipids and you should not have to rely on ATB to produce the lipid 
parameters, which will likely be less accurate than specifically 
parametrized entities.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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