Dr. Horn.
thank you for reaching out to assist.
This is my leap input file
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
Debarati
________________________________
From: Dr. Anselm Horn via AMBER <amber.ambermd.org>
Sent: Wednesday, August 3, 2022 7:33 PM
To: amber.ambermd.org <amber.ambermd.org>
Subject: Re: [AMBER] AMBER NME caps not recognized
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 - 13:38:11 PDT
