Yes I've sorted the histidine protonation issues out and almost finished building my system, thank you
One small final thing: When I used the saveamberparm command, LEaP warned me there were bonds formed that were between 3 and 16 angstroms long (Warning: there is a bond of ... angstroms between:) but didn't specify where these bonds were located/which atoms connected. When I've looked at the final PDB file (> savepdb complex ...) in VMD the structures/bonds etc of the protonated ligands all look correct. I reran the LEaP procedure with just my enzyme (no ligands) and there were no warnings. I've also looked at one of my ligands (Pyruvate with NADH cofactor) separately since my system has 4 of these ligands (tetramer enzyme-ligand complex) and the individual ligand system looks fine too.
Is this warning ignorable? VMD thinks there aren't any strange bonds present and the 'warning' quoted impossibly long bond lengths but not where said bonds were. To me it sounds like it tried to create these bonds but knew the lengths would be too long and didn't commit to it.
Sam
________________________________
From: Carlos Simmerling <carlos.simmerling.gmail.com>
Sent: 11 January 2021 22:09
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] LEaP Error/questions.
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%7C1a7b935f10b0415857e708d8b67dce03%7Cb52e9fda06914585bdfc5ccae1ce1890%7C0%7C0%7C637459998731485727%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=2i5S2UbET5OtNqBGkSLqqZ9KBEa6%2B8NyuXqK9%2BplVAI%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%7C1a7b935f10b0415857e708d8b67dce03%7Cb52e9fda06914585bdfc5ccae1ce1890%7C0%7C0%7C637459998731485727%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=2i5S2UbET5OtNqBGkSLqqZ9KBEa6%2B8NyuXqK9%2BplVAI%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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