On 1/23/13 12:48 PM, Shima Arasteh wrote:
I want to find the structure with the lowest RMSD, so I think it does not make
different to set any of pdb files as the ref structure.
I made an attempt and got the RMSD regarding the first pdb file. The RMSD
relative to -1 for the ref structure, is written in xvg file. Is my approach
logically correct?
The RMSD value should be positive, so I don't know how you get -1. Your
approach does not seem very sound - a structure does not have an absolute RMSD
value; it has an RMSD value relative to a reference structure, which must be
some sort of meaningful comparison or else you're not really measuring anything
useful.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
