Hi,
I have run into the same problems as Debarati.
The problem seems to be that the PDB atom names for NME were changed
with the most current AmberTools release, though I have not found this
change documented anywhere (... but also I didn't look look too hard,
might have missed it).
In the file aminoct12, the expected atom names now read "C" instead of
"CH3" and "H1"/"H2"/"H3" instead of "HH31"/"HH32"/"HH33".
Changing the atom names in the pdb file fixed the problem in my case.
Best regards,
Valentin
On 8/4/22 07:33, Dr. Anselm Horn via AMBER wrote:
> Debarati,
>
> this is strange, the atom names seem ok.
> Maybe there is a problem reading in the FF parameters?
>
> Please check (and maybe post) your tleap input commands (and output
> messages), where you setup the force field parameters.
>
> Best,
>
> Anselm
>
> Bioinformatik | NHR.FAU
> Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
> Germany
>
>
> On 08/04/2022 02:50 AM, Debarati DasGupta via AMBER wrote:
>> Hi all
>> I am stumped at this pdb I am trying to feed to AMBER for simulations.
>> Any ideas why the NME cap is not being recognized?
>> Error I am getting is this: see picture here
>> My NME residue looks like this:
>> [cid:154fd81a-307a-44dc-a2b8-eb7891647a98]
>>
>> [cid:947e3ba7-5dad-4be5-acaa-e67ff624a4d8]
>>
>>
>>
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Received on Thu Aug 04 2022 - 13:38:03 PDT
