On Wed, Jan 24, 2024, Shao, Qianzhen via AMBER wrote:
>
>I'm writing a python parser for .prmtop file right now. I'm having a hard
>time finding how prmtop record the chain-association for each residue.
>(i.e.: whether 2 residues are from the same chain)
>I will be grateful if anyone can share some insights.
Just to expand a bit: by default, (i.e. using saveAmberParm) the chainID's
are not included in the prmtop file. But you can use the "addPDB" command
in ParmEd to add these (plus other info like occupations and B-factors)
into the prmtop file.
Note that not every program that reads prmtop files knows how to use this
information, but cpptraj and some other scripts will recognize it.
That said, the "core" amber MD codes like pmemd and sander utilize
sequential residue numbers, so that the number alone uniquely identifies the
residue (and there is no need to combine chainID with residue number).
...good luck...dac
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Received on Wed Jan 24 2024 - 13:30:03 PST
