AMBER Archive (2008)

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

From: priya priya (priyaanand_27_at_yahoo.co.in)
Date: Thu Sep 25 2008 - 11:40:07 CDT

Thanks for your suggestion, the unusual amino acid(peptoid) is just a simple modification of amino acids, i have to delete a bond a create a bond and then save the pdb file for that. I will try both xleap and sirius program for that. Regards Priya ----- Original Message ---- From: Ross Walker <ross_at_rosswalker.co.uk> To: amber_at_scripps.edu Sent: Thursday, 25 September, 2008 8:25:21 PM Subject: RE: AMBER: to prepare pdb file fro unusual amino acid. 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 Unlimited freedom, unlimited storage. Get it now, on http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html/
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