AMBER Archive (2009)

Subject: Re: [AMBER] The PDB file was not recognized by Amber, what can i do?

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Dear Houyang,

Generally you can run babel (babel -ipdb crappy.pdb -opdb better.pdb).
That usually helps a bit.

In the literature people have used type 'CA' for carbon nanotubes (CNT).
See for instance
Hummer et al, NATURE | VOL 414 | 8 NOVEMBER 2001 | p188-190
Often using additional constraints to keep structure near experimental values.

I'm in the process of writing an article with parameters for some
carbon nanotubes for amber
(including vdw parameters). Preliminarily CA seems rather ok at least
for vdw parameters.
Hopefully this comes out in autumn.

To my experience antechamber cannot generate topology file (prep or
lib file) for CNT:s.
Instead one can use xleap and make connections by hand. In this way
one obtains the library file.

Terveisin, Markus

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• Previous message: Barbault Florent: "Re: [AMBER] The PDB file was not recognized by Amber, what can i do?"
• In reply to: Houyang Chen: "[AMBER] The PDB file was not recognized by Amber, what can i do?"
• Next in thread: Houyang Chen: "RE: [AMBER] The PDB file was not recognized by Amber, what can i do?"
• Reply: Houyang Chen: "RE: [AMBER] The PDB file was not recognized by Amber, what can i do?"
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