AMBER Archive (2008)

Subject: RE: AMBER: to prepare pdb file fro unusual amino acid.

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Sep 25 2008 - 01:36:08 CDT

Hi Priya,

 

How unusual is it? If it is a simple modification of an existing amino acid then this should be fairly easy to do in xleap. You just do something like:

 

Say for histidine

 

source leaprc.ff99SB

HIX = copy HIS

edit HIX

 

Then you can draw in / delete atoms, set the atom types etc. You will of course need to calculate the charges for this amino acid, add any missing parameters before you can simulate it in AMBER. If the amino acid is more complicated then you probably want to use a program more suited to 3D drawing - http://sirius.sdsc.edu works well.

 

I suggest you take a look at Tutorial A1 - http://ambermd.org/tutorials/ for some examples. Tutorial B6 also provides a tutorial on Sirius.

 

Good luck,

Ross

 

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of priya priya
Sent: Wednesday, September 24, 2008 1:03 AM
To: amber_at_scripps.edu
Subject: AMBER: to prepare pdb file fro unusual amino acid.

 

Hi Amber Users,

I am looking for some way to prepare pdb files for a molecule with unusual amino acid, that is not incluede in Xleap of Amber.
Can anybody suggest me some tool that can be use to draw the molecule.

Regards
Priya Anand

  _____

Bollywood news, movie reviews, film trailers and more! Click <http://in.rd.yahoo.com/tagline_movies_1/*http:/in.movies.yahoo.com/?wm=n/> here.

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu