Thank you for the clarification.
On Wed, Apr 6, 2022 at 2:53 PM David A Case <david.case.rutgers.edu> wrote:
> On Wed, Apr 06, 2022, Hrishikesh Dhondge wrote:
> >
> >I have a doubt regarding the use of the amber force field with NAMD. If I
> >have to use the amber force field in NAMD, then I can create the system in
> >the leap program provided by AMBER. But the leap program renumbers the
> >residues in the simulation system. Chain identifiers are not used. There
> is
> >a single list of all atoms where atoms and residues are numbered
> >sequentially starting from 1 without any gaps.
> >
> >So if I have a protein-RNA/DNA complex to simulate, will it affect the
> >simulation (missing information about chain or segment identifiers)?
>
> As Vlad said, the simulation should be fine. The following band-aid will
> allow analysis to be used with the original residue numbers and chainIds"
>
> use the addPDB action in parmed to put information from the original
> PDB file into your tleap-created prmtop file
> then you can use cpptraj and ambpdb (which is built on top of cpptraj)
> to run analyses or create new PDB files that have the original
> information
>
> It is worth making the distinction between a 'residue index' (which starts
> at 1 in increments for each new residue), and a 'residue number' (which is
> assigned by the creator of the PDB file, and has relatively few rules.)
>
> Back in pre-history, Amber code made the mistake of treating the latter as
> the former. But the addPDB approach solves a lot of the problems that this
> created.
>
> ....dac
>
>
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--
With regards
Hrishikesh Dhondge
PhD student,
LORIA - INRIA Nancy
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Received on Wed Apr 06 2022 - 06:30:02 PDT
