On Fri, Sep 09, 2016, Chitrak Gupta wrote:
>
> I am trying to generate topology file for a non-standard amino acid. It is
> extremely similar to glutamic acid, just an extra CH2 moiety added to the
> side chain. The residue name is AAD and has a total charge of -1. I am
> following the amber tutorial B5.
It's not clear how closely you are following the tutorial...the "AAD" residue
in the components.cif file is nothing like a modified glutamic acid. If you
used the AAD unit in that file, you will certainly get very weird results.
For a simple analogue like you describe, the R.E.D. server is probably the
most straightforward way to proceed--maybe this modification is already in
their database.
Or, you can follow tutorial B5 with the correct residue identifier. Be sure
to visualize each step (e.g. convert the prepin to pdb and look at it in a
molecular viewer) to be sure you are getting the results you want.
....good luck....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Sep 10 2016 - 10:00:03 PDT
