AMBER Archive (2006)

Subject: Re: AMBER: ambpdb and original PDB

From: snoze pa (
Date: Mon Apr 17 2006 - 13:48:55 CDT

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.

thanks a lot your help and time.
best snoze

On 4/17/06, Ross Walker <> wrote:
> See section 5 of this tutorial for how to do an RMSD alignment with VMD:
> 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 |
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> ------------------------------
> *From:* [] *On
> Behalf Of *snoze pa
> *Sent:* Monday, April 17, 2006 11:20
> *To:*
> *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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