Hi Valentin and Debarati,
The changes were made to have the atom names match up with the .cif format
for the residues. For NME this was the change from CH3, HH31/2/3 to C,
H1/2/3.
Was the PDB used downloaded recently from the PDB database? There might be
something overlooked on my part. Alternatively, we can make this backward
compatible.
On Thu, Aug 4, 2022, 4:18 AM Valentin Hörschinger via AMBER <
amber.ambermd.org> wrote:
> 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 - 13:38:07 PDT
