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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Received on Wed Apr 06 2022 - 06:00:03 PDT
