Date: Wed, 10 Jul 2024 00:49:04 +0000
From: "Wang, Junmei" <JUW79.pitt.edu>
Subject: Re: [amber.ambermd.org: Re: [AMBER] Gaff Atom Type Duplicates, With
Different Data]
All those parameters are correct. We used a smart way to incorporate bond
information into atom types. cc-cc and cd-cd are single bonds, while cc-cd
are double bonds. Similarly, cc-nc and cd-nd are single bonds, while cc-nd
or cd-nc are double bonds.
As cc/cd and nc/nd are equivalent, cc-nd and cd-nc have the same parameter,
so do cc-cc and cd-cd. I think I solved the duplication issue a long time
ago.
All the best,
Junmei
On Thu, Jul 4, 2024, 12:30 PM Warren, Kyle Benjamin via AMBER <
amber.ambermd.org> wrote:
> Hi all,
>
> I'm trying to generate new parameters for a molecule I'm trying to run
> molecular dynamics simulations on within AMBER, however, I've run into a
> snag. In the gaff2.dat file. it states atom types "cc" and "cd" are the
> same, and the same situation with "nc" and "nd". However, when I inspect
> interaction angle information between each combination of "identical" atom
> types, there is different data listed when based on atom descriptions,
> these interactions in theory should all be identical.
>
> Here is interaction information pulled directly from the gaff2.dat file:
>
> nc-cc-nd 73.39 124.94 2021 95 4.6365
> nc-cc-nc 72.32 124.41 2021 3 1.6098
> nc-cd-nc 110.8 128.07 SOURCE4_SOURCE5 10 0.4198
> nc-cd-nd 75.96 115.74 2021 308 1.2372
> nd-cc-nd 73.85 128.00 2021 10 0.4198
>
> Here are gaff2.dat's atom descriptions for these cases
> [image: Screenshot 2024-07-04 145340.png]
> [image: Screenshot 2024-07-04 145420.png]
>
> Is there a practice or methodology I should be following when assigning my
> atom types for these cases where assigning atom types is ambiguous (I.e.
> when picking between cc and cd is unclear)? Any help/clarification on this
> would be greatly appreciated. Additionally, if anyone could help me
> understand the meaning of "non-pure aromatic system" versus "pure aromatic
> system", it would be greatly appreciated, I'm assuming "system" is
> referring to the whole molecule, but I am not certain.
>
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Received on Thu Jul 11 2024 - 14:00:02 PDT
