A good step might be to build it first without ligand or cofactor, just to
make sure the protein/water/ions setup is good. Then add in the other
molecules.
you'll want to check and make sure that the atom names in the NADH match
those in the library, it's possible that they don't but you should see that
in the Leap output. Again, it's easier to do that if you got the protein
part working already.
On Mon, Jan 11, 2021 at 12:10 PM Sam Walsworth (Researcher) <
Sam.Walsworth.hud.ac.uk> wrote:
> Hi David
>
> I played around with the original PDB file and using pdb4amber and it
> mostly worked, except now I have HIE atoms not having a type (I believe
> I've seen issues regarding histidine protonation causing errors) and the
> NADH cofactor atoms types are not found. I'm using Ross Walker's
> contributed parameters for these
> ($AMBERHOME/dat/contrib/NADH_and_NAD+/NADH.lib) so I think I'm just missing
> a step in loading these into LEaP correctly.
>
> I'm using ff99SB because the simulations I'm recreating initially to learn
> how to deal with these enzyme-ligand complexes used it too. I have seen
> papers on ff14SB and ff19SB improving on ff99SB however
>
> Sam
> ________________________________
> From: David A Case <david.case.rutgers.edu>
> Sent: 11 January 2021 13:29
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] LEaP Error/questions.
>
> On Mon, Jan 11, 2021, Sam Walsworth (Researcher) wrote:
> >
> >When you load a complex into LEaP using complex = loadpdb ... does that
> pdb
> >file have to be all atoms or just the coordinates of the heavy
> non-hydrogen
> >atoms?
>
> It generally matters very little, since leap will add build in hydrogens in
> standard positions if they are missing.
>
> >
> >Also I got fatal errors saying atom does not have a type when I tried to
> >create parameters.
>
> You mention "complex": do you have a ligand or other non-standard
> component?
> Look at the "Developing non-standard parameters" at the tutorial tab on the
> Amber web page, especially tutorial 2.1 (if you have a ligand.)
>
> ...good luck...dac
>
>
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Received on Mon Jan 11 2021 - 10:00:02 PST
