Debarati,
sorry, my mistake: I had looked into the Amber20 libs (which were at
hand) instead of the Amber22 libs.
So, your issue seems to be solved, as Valentin pointed out: simply
rename your atoms in the input pdb file according to the new naming
scheme, then it should work fine.
Best,
Anselm
On 08/04/2022 05:38 PM, Debarati DasGupta via AMBER wrote:
> Hello Kellon
> I am not sure as I was provided with the Maestro prepped.pdb file to put to AMBER simulations, hence no idea of the source at this point.
> However I will follow up with Valentim and change the atom names of NME to make sure it reads it correctly.
> My leap input is as follows:
>
> source leaprc.gaff2
> source leaprc.water.tip3p
> source leaprc.protein.ff19SB
> prot=loadpdb test.pdb
> solvatebox prot TIP3PBOX 12
> addions prot Cl- 0
> addions prot Na+ 0
> charge prot
> savepdb prot solvated.pdb
> saveamberparm solvated.prmtop solvated.crd
>
> ________________________________
> From: Kellon Belfon via AMBER <amber.ambermd.org>
> Sent: Thursday, August 4, 2022 2:49 AM
> To: Valentin Hörschinger <valentin.hoerschinger.uibk.ac.at>; AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] AMBER NME caps not recognized
>
> 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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>>>>
>>>
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Received on Thu Aug 04 2022 - 13:38:15 PDT
