AMBER Archive (2004)

Subject: Re: AMBER: build a cyclic peptide

From: Eric Hu (yhu_2003_at_yahoo.com)
Date: Wed Nov 24 2004 - 12:26:44 CST

I did build the top and crd files with a long bond
between two ends by using "bond" command. However, the
minimization does not result in a reasonable
structure.

Eric
--- Carlos Simmerling <carlos_at_ilion.bio.sunysb.edu>
wrote:

> you might want to try the bond command. I don't
> think that Leap will be able
> to bulld reasonable initial coordinates, though. if
> you don't have any
> you can
> minimize the linear one but look out for cis peptide
> bonds and chirality
> flips.
>
>
===================================================================
> Carlos L. Simmerling, Ph.D.
> Associate Professor Phone: (631) 632-1336
> Center for Structural Biology Fax: (631) 632-1555
> Stony Brook University Web:
> http://comp.chem.sunysb.edu/carlos
> Stony Brook, NY 11794-5115 E-mail:
> carlos.simmerling_at_stonybrook.edu
>
===================================================================
>
>
>
>
> Eric Hu wrote:
>
> >Hi, I wonder if there is a way to build a cyclic
> >peptide in leap. "sequence" seems to give a linear
> one
> >only. Thanks.
> >
> >Eric
> >
> >
> >
> >__________________________________
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