AMBER Archive (2006)

Subject: Re: AMBER: RMS

From: carlos (carlos_at_csb.sunysb.edu)
Date: Mon Apr 03 2006 - 16:18:24 CDT

I'm not sure what nts are, but in ptraj you can use
the rms command and say "nofit" at the end. this will
leave the structure at the previous fit. so, do a regular
rms command fitting to 1-10, then do rms for 50-60 with nofit
at the end of the line.

Wen Li wrote:
> I was hoping someone could help me on the following question:
>
> I have one molecule (100 nts) in 100 conformaions so in 100 pdb files. How
> can I find rmsd of nts 50-60 of each conformation relative to nts 50-60 in
> reference conformation when every conformation is aligned to the reference
> at nts 1-10.
>
> Thanks,
> Wen
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu