Thank you so much, that helped!
WE ARE REACHING THE STAGE WHERE THE PROBLEMS WE MUST SOLVE ARE
GOING TO BECOME INSOLUBLE WITHOUT COMPUTERS.
I DO NOT FEAR COMPUTERS. I FEAR THE LACK OF THEM.
-- ISSAC ASIMOV
________________________________________
From: David A Case [case.biomaps.rutgers.edu]
Sent: Thursday, March 21, 2013 7:29 AM
To: AMBER Mailing List
Subject: Re: [AMBER] How to use AMBER parameters for modified amino acids
On Wed, Mar 20, 2013, Symon Gathiaka wrote:
>
> I have amber parameters (from a paper) for a modified amino acid in a
> protein of interest but could not find any help from the tutorials how
> to go about creating the inputs for sander.
>
> What am asking is, since i have the library file, how do i go about
> creating the force field modification file (.frcmod) to load into tleap
> considering that its only for one modified residue in a peptide?
The format of the frcmod file is described here:
http://ambermd.org/formats.html
You make a frcmod file by hand. LEaP will complain if something is missing.
You can also use ParmEd to examine the resulting prmtop file to make sure that
you have what you want.
....dac
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Received on Sat Mar 23 2013 - 11:00:02 PDT
