Re: [AMBER] About md parameters for unuaual amino acid residues

From: Jason Swails <>
Date: Tue, 15 Jun 2010 01:44:27 -0400


HYP is defined in the GLYCAM_amino_06.lib file. To get access to this
modified amino acid, load this library

loadoff GLYCAM_amino_06.lib

I'm assuming the charges for HYP were defined in the same way (RESP with
HF/6-31 G*).

Hope this helps,

On Tue, Jun 15, 2010 at 1:12 AM, Rilei Yu <> wrote:

> Dear amber users,
> Recently, I am doing MD simulation on a system that contains some special
> residues, for example, HYP. Unfortunately, I could not use amber10 simulate
> this system (Maybe I did not load the relevant forcefield). So I just did
> everything as the tutorial did, and could run MD on my system. Although, it
> works well now, I am still interested in parameters of these abnormal
> residues. After all, I am not so confident at the accuracy of the parameters
> obtained based on manually editing (for exp, using antechamber). If the
> parameters has appeared, I hope everyone here can inform me.
> I am really apppreciated for your help!
> Rilei Yu
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Mon Jun 14 2010 - 23:00:03 PDT
Custom Search