AMBER Archive (2004)

Subject: Re: AMBER: build a cyclic peptide

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Wed Nov 24 2004 - 14:33:10 CST

is the energy going down still? meaning is the minimizer stuck, or is it
just taking a while? sometimes if you minimize a bad structure, things like
side chains get trapped and you can't get the bond shorter because the
side chains are getting compressed. looking at the structure might help.
you can send me a pdb of the minimized structure if you want me to take
a quick look at it.
carlos

===================================================================
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:

>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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>
>
>
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