Hi,
Currently there is no RMSIP calculation in cpptraj, although one is
planned (thank you for the reminder!).
Note you will probably have to modify the provided script to make it
work with cpptraj/ptraj-generated "evecs" files (i.e. the output from
the 'analyze matrix' command). The format of the evecs file is:
<Title>
<# avg. coords> <vector size>
<Average coordinates, 7 columns>
****
<vector 1> <eigenvalue 1>
<eigenvector, 7 columns>
****
<vector 2> <eigenvalue 2>
and so on for each eigenvalue/eigenvector. The key here is that
eigenvectors can span multiple lines if you have more than 2 atoms
(i.e. 6 coordinates), which is almost always the case, so the script
needs to take this into account. Every eigenvalue/eigenvector is
preceded by '****', which should make scripting easier. Good luck,
-Dan
On Sat, May 17, 2014 at 9:54 AM, Yip Yew Mun <yipy0005.gmail.com> wrote:
> Hi, I really really would appreciate any help given.
>
> I understand that in the archives, someone tried asking for help on a script to calculate RMSIP after doing PCA using ptraj in 2008. However, there was completely no response to it. While the formula for RMSIP is well known in literature, I’m unable to generate a bash script to process the eigenvectors from PCA to calculate RMSIP. Therefore, I’m hoping if there is anyone who is willing to share his/her script on calculating RMSIP.
>
> Your help is very very much appreciated.
>
> Regards
> Yip Yew Mun
> Graduate, PhD
> Chemistry and Biological Chemistry
> School of Physical and Mathematical Sciences
> Nanyang Technological University
>
>
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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) 585-6208 (Fax)
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Received on Mon May 19 2014 - 07:30:03 PDT
