Hi,
My guess is that you would like not only to preserve the chain ID of
each atom record, but be able to e.g. select atoms by chain ID during
analysis with cpptraj/ptraj? It's an idea I've thought about, and
there are actually tentative plans to expand the mask parser for the
next release of cpptraj. I'll consider this feature formally
requested...
-Dan
On Mon, Oct 15, 2012 at 1:45 PM, David A Case <case.biomaps.rutgers.edu> wrote:
> 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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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Wed Oct 17 2012 - 07:30:05 PDT
