AMBER Archive (2006)

Subject: Re: AMBER: ambpdb and original PDB

From: Mingfeng Yang (mfyang_at_gmail.com)
Date: Mon Apr 17 2006 - 15:05:43 CDT

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.

In most cases, I think people only care about the conformations of the
structure which are decided by the intramolecular distances only. The
orientation of the molecules are not important. For example, superimposition
or not won't change the radius of gyration of your conformations.

Mingfeng

> thanks a lot your help and time.
> best snoze
>
> On 4/17/06, Ross Walker <ross_at_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_at_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_at_scripps.edu [mailto:owner-amber_at_scripps.edu] *On
> > Behalf Of *snoze pa
> > *Sent:* Monday, April 17, 2006 11:20
> > *To:* amber_at_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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