Re: [AMBER] Problem related with the Ptraj

From: Carlos Simmerling <>
Date: Sat, 4 Jun 2011 07:17:38 -0400

Yes this means atoms named CA. you can add other names too such as .CA,N,C.
Look in thr manual for more details.
On Jun 4, 2011 7:14 AM, "Sindrila Dutta banik" <> wrote:
> Hello!
> I am using ptraj to get a plot RMSD vs time. For this I have prepared a
script file as described in the user manual. But it is not clear to me why I
should write '.CA'. Is this is mean the RMD deviation with respect to the C
alpha atom?
> If I want to know the RMS deviation with respect to the backbone of
protein chain what should I write in the script file?
> With my best regards
> Sindrila
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Received on Sat Jun 04 2011 - 04:30:04 PDT
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