On Monday 17 April 2006 14:48, snoze pa wrote:
> Thanks Ross for quick reply. I am up with some solution to my problem.
> Just an extention to my previous query. In my case the final MD
> structure seems to be slightly moved(tilted) away from the original
> minimized structure. First MD was for 1ns and then for 2ns. In both
> situations the final structure is tilted from the original structure, which
> is due to a large loop region. I want to analyse my data. Which one
> is proper way
>
> 1. Analyse the data based on MD output as it or
> 2. Analyse the data after overlaping the final MD struture into PDB file
> obtained from minimization. In this case I also calculated the
> rmsd and it is 1.4.
What kinds of analysis do you want to carry out? You gotta be more specific,
if you really want people to provide help.
Even for a simple structural comparison, there are lots of methods.
For RMSD, you certainly need to do superimposition.
For measurements based on intramolecular distances, it's unnecessary.
Best,
Mignfeng
>
> thanks a lot your help and time.
> best snoze
>
> On 4/17/06, Ross Walker <ross.rosswalker.co.uk> wrote:
> > See section 5 of this tutorial for how to do an RMSD alignment with VMD:
> > http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_nine/index.
> >htm
> >
> > This will let you compare the two structures. Alternatively you can do it
> > with ptraj to create a pdb that is rmsd aligned to the original
> > structure.
> >
> > All the best
> > Ross
> >
> >
> > /\
> > \/
> >
> > |\oss Walker
> > |
> > | HPC Consultant and Staff Scientist |
> > | San Diego Supercomputer Center |
> > | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> > | http://www.rosswalker.co.uk | PGP Key available on request |
> >
> > Note: Electronic Mail is not secure, has no guarantee of delivery, may
> > not be read every day, and should not be used for urgent or sensitive
> > issues.
> >
> >
> > ------------------------------
> > *From:* owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] *On
> > Behalf Of *snoze pa
> > *Sent:* Monday, April 17, 2006 11:20
> > *To:* amber.scripps.edu
> > *Subject:* AMBER: ambpdb and original PDB
> >
> > Hi,
> > After minimization, i generate a PDB file using ambpdb, but the center
> > of PDB coordinate from ambpdb seems to different from the original PDB
> > file. Is it okie, because I want to compare the changes in my original
> > PDB file after minization. If yes then how can I overlap these two
> > structures? thanks in advance
> > snoze
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Received on Tue Apr 18 2006 - 03:02:43 PDT
