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
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Received on Mon Aug 08 2022 - 07:00:02 PDT
