hi,
tq Mr. Daniel Roe
I was using ptraj in order to generate the pdb file form mdcrd file. Very messy means the bonds appear stretched. so, may i know why it happens?
________________________________
From: Daniel Roe <daniel.r.roe.gmail.com>
To: fatahiya <fatahiyamohdtap.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Thursday, 22 September 2011 7:42 PM
Subject: Re: [AMBER] RMSD
Hi,
In order to help you out some more information is needed about exactly
what you have done. What procedure did you use to generate the PDB
file? What does "very messy" mean (i.e. do bonds appear stretched, in
the wrong places, etc?).
On Thu, Sep 22, 2011 at 2:13 AM, fatahiya <fatahiyamohdtap.yahoo.com> wrote:
> structure that i was download form pdb web. The no. of atom for my model is 210, the no.of atom for reference is 203.
This will certainly cause problems for both Amber and VMD RMSD
functions; the number of atoms in your reference has to be the same as
in your target structure (atom ordering must be the same as well).
It's not unusual for PDB files to be missing some parts of a structure
(like terminals residues in a protein for example), in which case you
can just calculate the RMSD of the parts of the structure that
overlap. However, without knowing anything more about your system it's
difficult to make specific recommendations.
-Dan
> can anybody tell me how these problems occur and how i want to do the rmsd alignment?
>
>
> -fatahiya-fatahiyamohdtap.yahoo.com
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Received on Sun Sep 25 2011 - 22:30:03 PDT
