[gmx-users] Problem with topology generation by Amber 12 ff

[Amir Zeb]

Thanks Dr. Justin,

The atoms of Histidine residue formed the dihedral CB, CG, ND1 and CD2.
Tracing the residues rtp file in Amber12 ff, I should assign His either HID
or HIE, But once I protonate HIS at NE2 only and assign this NE2-protonated
HIS as HIE, some of the residues other than this particular HIS also read
as HIE by the force filed itself and I should assign them as HIE, because
otherwise I will get the same error as mentioned above.

Thanks for your consideration!

On Mon, Dec 4, 2017 at 6:25 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/4/17 1:45 AM, Amir Zeb wrote:
>
>> Hello gmx users,
>>
>> I have generated topology and coordinate files of ZN metalloprotein by
>> Amber 12 ff. Now I am facing this following issue at grompp run:
>>
>> "ERROR 1 [file topol_Protein_chain_A.itp, line 49741]:
>>    No default Improper Dih. types"
>>
>> If I use another ff like Amber99SB- ILDN, there is no such error. I
>> searched out the solution on google but could not find the answer.
>>
>> Please help me how to fix this issue?
>>
>
> Which atoms are in that interaction on that line, and should there be such
> an interaction there?
>
> -Justin
>
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