are you wanting to renumber them before Leap? did you try it?
Leap will have trouble with this, it will try to split residue apart that
have different names, and it will ignore duplicate atom names in a residue
(thinking they might be alternate conformations). See this message in leap:
Atom names in each residue should be unique. (Same-name atoms are handled
by using the first occurrence and by ignoring the rest. Frequently
duplicate atom names stem from alternate conformations in the PDB file.)
I don't think this will make analysis easier, it could be harder. For
example, you can't refer to an atom by residue number and name, since it
isn't unique.
can you tell us more about what exactly you're trying to achieve? If it's
about molecule numbering, that can be adjusted separately...
On Thu, Dec 17, 2020 at 5:45 AM Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
> Realising that some additional information would make it a lot easier to
> answer.
>
> I am constructing a short peptide using LEaP and saving it as a PDB file.
>
> Constructing a simulation system I have the option to renumber residues
> sequentially in the produced system PDB file. I can leave the peptide in
> the system PDB numbered from 1-4 and then the next molecule starting at 5
> and onwards. Or I could renumber the entire peptide as residue 1 and then
> continue with 2 and so forth.
>
> This could make life somewhat easier when preparing input for analyses
> later on, especially if there are numerous peptides in the same simulation.
> I got a bit concerned though thinking about what would happen if trying to
> use (for example) “bond” in leap, it would involve setting the bond between
> 1 and 1.
>
> Rather than trying to exhaust any concern I can think up I though I would
> ask and see of someone else had already done this and could provide some
> suggestion if I should maintain residue numbering in peptides from leap or
> renumber.
>
> Best regards
> // Gustaf
>
> > On 17 Dec 2020, at 11:29, Gustaf Olsson <gustaf.olsson.lnu.se> wrote:
> >
> > Would there be any obvious problem with renumbering AAs in a peptide to
> a single residue number?
> >
> > LEaP output for a 4 AA peptide gives residues 1-4 as one molecule.
> Changing this to residue 1 for all AAs, can this cause any
> unintended/unexpected issues?
> >
> > Best regards
> > // Gustaf
> >
> >
> >
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Received on Thu Dec 17 2020 - 04:00:02 PST
