see that paper - OPC performs better, but we have not published testing
across many water models.
On Thu, Aug 4, 2022 at 2:53 PM Debarati DasGupta <
debarati_dasgupta.hotmail.com> wrote:
> Hello Prof Simmerling,
> What would you suggest me to use? Any specific recommendations?
> Sincerely,
> Debarati
>
> ------------------------------
> *From:* Carlos Simmerling <carlos.simmerling.gmail.com>
> *Sent:* Thursday, August 4, 2022 7:31 AM
> *To:* Debarati DasGupta <debarati_dasgupta.hotmail.com>; AMBER Mailing
> List <amber.ambermd.org>
> *Cc:* Dr. Anselm Horn <anselm.horn.fau.de>
> *Subject:* Re: [AMBER] AMBER NME caps not recognized
>
> as a side note - make sure that combining ff19SB with TIP3P water is
> really what you want to do. That combination may produce very helical
> structures.
> https://pubs.acs.org/doi/10.1021/acs.jctc.9b00591
>
>
>
> On Thu, Aug 4, 2022 at 11:39 AM Debarati DasGupta via AMBER <
> amber.ambermd.org> wrote:
>
> 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]
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
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Received on Thu Aug 04 2022 - 13:38:18 PDT
