AMBER Archive (2004)

Subject: Re: AMBER: A general question

From: aini_at_UMDNJ.EDU
Date: Tue Feb 03 2004 - 19:39:44 CST

Dear Dr. Simmerling,

  Thank you for your answer. However it is not clear for me. Can you give
more details? I tried to search through amber archives and found out
nothing because of lack of proper keywords.
Thank you very much!

aini

Quoting Carlos Simmerling <carlos_at_csb.sunysb.edu>:

> 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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