Re: AMBER: build a cyclic peptide

From: Carlos Simmerling <>
Date: Wed, 24 Nov 2004 13:56:57 -0500

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.

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
>--- Carlos Simmerling <>
>>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
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Received on Wed Nov 24 2004 - 19:53:00 PST
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