AMBER Archive (2004)Subject: Re: AMBER: build a cyclic peptide
From: Eric Hu (yhu_2003_at_yahoo.com)
Date: Wed Nov 24 2004 - 14:11:18 CST
Yes, the bond is still long and energy is still high
(~100kcal/mol) even after 5000 NCYC. Thanks.
Eric
--- Carlos Simmerling <carlos_at_ilion.bio.sunysb.edu>
wrote:
> Eric,
> what do you consider "reasonable"? Do you mean bonds
> are still long,
> or highly distorted angles, or just not a good low
> energy conformation?
> If you can provide more details we may be able to
> make suggestions.
> Carlos
>
> Eric Hu wrote:
>
> >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.
> >>
> >>
> >>
> >>
>
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