does your file have hydrogen atoms? most PDB files do not.
There are tools, such as H++, that help you decide if HID or HIE is a
better match for each HIS and rename them accordingly.
On Mon, Jan 11, 2021 at 3:58 PM Sam Walsworth (Researcher) <
Sam.Walsworth.hud.ac.uk> wrote:
> Hi all
>
> Thank you for the help. I've come to realise when I swapped HIS to HIE to
> match residue names I was getting a single hydrogen that didn't match HIE
> lib file and did match HID. When I changed HIE to HID in the PDB file I was
> now getting other hydrogens, one per residue/multiple residues, that didn't
> match the HID lib file. I'm now working on the assumption that my enzyme
> has histidines both HID and HIE.
>
> Is this common and is there a way of determining which HIS are HID or HIE
> without inspecting error messages and comparing PDB and lib files?
>
> Thank you in advance
>
> Sam
> ________________________________
> From: Maria Nagan <maria.c.nagan.gmail.com>
> Sent: 11 January 2021 17:37
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] LEaP Error/questions.
>
> Hi Sam,
>
> You want your pdb residue name to match the lib file name for the residue.
>
> 1) Here’s a link to the tutorial on building a protein system in explicit
> solvent:
>
> https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fambermd.org%2Ftutorials%2Fbasic%2Ftutorial7%2Findex.php%23Protonation_states_&data=04%7C01%7CSam.Walsworth%40hud.ac.uk%7Cd6d48cafdb104aed879308d8b657c4d0%7Cb52e9fda06914585bdfc5ccae1ce1890%7C0%7C0%7C637459835382516237%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=n0nVzFUCDbO6%2FgNJeAhg3GxKJPlanjXFNVu2Gj2WYLQ%3D&reserved=0
> <
> https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fambermd.org%2Ftutorials%2Fbasic%2Ftutorial7%2Findex.php%23Protonation_states_&data=04%7C01%7CSam.Walsworth%40hud.ac.uk%7Cd6d48cafdb104aed879308d8b657c4d0%7Cb52e9fda06914585bdfc5ccae1ce1890%7C0%7C0%7C637459835382526229%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=vOtoMZRHNDXf0aRwrOH2kfBwKRu3PD6IaSWk1%2FdBWGA%3D&reserved=0
> >
>
> Also, if you just have HIS, leap needs to know is it HIE or HID, etc. It
> defaults to making HIS —> HIE (specified at end of leaprc file).
>
> 2) In leap you loaded $AMBERHOME/dat/leap/cmd/oldff/leaprc.ff99SB, right?
> leaprc.ff99SB loads $AMBERHOME/dat/leap/lib/all_amino94.lib. Those are the
> amino acid residue names leap expects (those loaded from the lib file).
> Same issue with your NADH.lib file. The pdb name needs to match your
> NADH.lib.
>
> Residue names are the same in ff19SB.
>
> Maria
>
> > On Jan 11, 2021, at 12:10 PM, Sam Walsworth (Researcher) <
> Sam.Walsworth.hud.ac.uk> wrote:
> >
> > Hi David
> >
> > I played around with the original PDB file and using pdb4amber and it
> mostly worked, except now I have HIE atoms not having a type (I believe
> I've seen issues regarding histidine protonation causing errors) and the
> NADH cofactor atoms types are not found. I'm using Ross Walker's
> contributed parameters for these
> ($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 - 14:30:02 PST
