AMBER Archive (2009)

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

From: Houyang Chen (houyangchen2008_at_hotmail.com)
Date: Wed Apr 29 2009 - 17:17:51 CDT

Hi, everyone,

 

Thanks so much.

I will read more tutorials you suggested first.

 

Terveisin Markus, when you article publish, please let me know and i want to download it.

Best,

 

Houyang

 

> Date: Wed, 29 Apr 2009 10:16:30 +0300
> Subject: Re: [AMBER] The PDB file was not recognized by Amber, what can i do?
> From: markus.kaukonen_at_iki.fi
> To: amber_at_ambermd.org
>
> 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
>
>
>
> --
> --www=http://www.iki.fi/markus.kaukonen
> --Markus.Kaukonen_at_iki.fi
> --office: N102 Nano building FIN-02015 TKK
> --home: Viinirinne 3 F 12, 02630 Espoo, FIN
> --tel: h 045-1242068, w 4518694, 050-5112785
> --Rikos ei kannata, eika maatalous
> --Suomessa. (Paimio 1998) ---
>
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