PS - You can use the '::' (colon colon) mask operator to select via
chain ID and the ':;' (colon semicolon) mask operator to select by
"original" residue number. So after you've set your chain IDs etc, to
select the metal in either system you would use "::B".
On Mon, Aug 8, 2022 at 9:32 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> Hi,
>
> On Fri, Aug 5, 2022 at 1:41 PM Murray, Makay via AMBER
> <amber.ambermd.org> wrote:
> >
> > How do I change the resid numbers in the odd ball system to match the other systems?
> >
> > I’ve seen the function “change” in the cpptraj section 34.9.4 in amber22.pdf. It’s function “oresnums” is very close to what I want but not quite.
>
> How exactly does the 'oresnums' functionality not work for you?
>
> Just to clarify, cpptraj is aware of two different kinds of numbering.
> The "residue number" is the internal residue index starting from 1.
> This just a function of the system's topology and can't be changed.
>
> The "original residue number" (maybe unfortunately named but it is
> what it is) can also be thought of as "PDB residue numbering". This is
> what the 'oresnums' functionality lets you change. You can also change
> the chain ID (via 'chainid') and insertion code (via 'icodes').
>
> What I would do in your situation is distinguish the nucelotides and
> the metal via a combination of original residue numbering and chain
> ID. For the original system:
>
> change chainid of :1-15 to A
> change chainid of :16 to B
> change oresnums of :1-15 min 1 max 15
> change oresnums of :16 min 1 max 1
>
> For the "oddball" system:
>
> change chainid of :2-16 to A
> change chainid of :1 to B
> change oresnums of :2-16 min 1 max 15
> change oresnums of :1 min 1 max 1
>
> Hope this helps,
>
> -Dan
>
>
>
> >
> >
> >
> > Does anyone know of a method to edit the #Res value? Thanks!
> >
> > -Makay
> > PhD Candidate
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Aug 08 2022 - 07:00:04 PDT
