AMBER Archive (2004)

Subject: Re: AMBER: A general question

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Tue Feb 03 2004 - 18:13:09 CST

if you are using parm94 or parm99, formation
of helix may indicate a force field problem.
this has been documented in the literature, check the
amber archives.
carlos

----- Original Message -----
From: <aini_at_UMDNJ.EDU>
To: <amber_at_scripps.edu>
Sent: Tuesday, February 03, 2004 6:49 PM
Subject: AMBER: A general question

> Dear Ambers,
>
> I have a general question about MD simulation. Is it possible to observe
> secondary structure formation (e.g. helix) from a loop during the MD
> simulation? I am running a simulation on protein-ligand complex. I found
> out a extra short helix formed in our average structure after 500 ps GBSA
> simulation.
>
> Thank you very much!
> aini
>
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