Re: [AMBER] Maintaining Chain ID

From: David A Case <>
Date: Mon, 15 Oct 2012 15:45:36 -0400

On Mon, Oct 15, 2012, Brown, Kyle wrote:

> What is the best way to generate prmtop and inpcrd files from a PDB file
> and maintain Chain Ids (e.g. A,B,C…) for subsequent analysis of a
> trajectory?

The add_pdb program (see $AMBERHOME/AmberTools/src/xray) will add such
information to the prmtop file, which is the first step. Second step is to
get such information back out for analysis. If you just want to get a PDB
file out with the original residue numbers and chain_ids, then use ambpdb
(with the prmtop modified by add_pdb).

If you want some other sort of analysis, you may have to write your own
program, or post a feature request to this mailing list. I'm betting Dan Roe
would be willing to modify cpptraj if he had specific ideas of what people
wanted it to be able to do.

[Warning: I don't think add_pdb has been used a lot; so you may find some
rough edges.]

...good luck...dac

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Received on Mon Oct 15 2012 - 13:00:07 PDT
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