AMBER Archive (2008)

Subject: Re: AMBER: Trans proline

From: Brent Krueger (kruegerb_at_hope.edu)
Date: Sat Aug 02 2008 - 22:47:16 CDT

Hey Adrian,

I'm finally getting to clearing out old emails from when we were packing,
then driving from SD to Michigan, then unpacking, then cleaning our house
and so forth.

This email got me thinking about a poly-proline paper that we had started
about a year ago. Where are we on that? Is it dead completely, or can we
revive it?

Cheers,
Brent

On Sun, Jul 20, 2008 at 8:27 AM, Adrian Roitberg <roitberg_at_qtp.ufl.edu>wrote:

> I am also confused.
>
> tleap by default will do trans proline, for sure.
>
> in fact, cis prolines are VERY rare in nature, maybe under 5% in the pdb.
>
> a.
>
>
> Carlos Simmerling wrote:
>
>> are you sure that leap only adds cis proline?
>> I have never experienced that myself, leap by default builds trans only.
>> you may be able to use the leap "impose" command to build
>> the alternate.
>>
>> On Sun, Jul 20, 2008 at 1:53 AM, dipti lele <diptisl86_at_gmail.com> wrote:
>>
>>> Hello .
>>> I have to make a peptide with trans proline into it. How should I go
>>> about it using tleap? Are there any parameter files for trans proline
>>> available? By default tlarp added cis proline only. But NMR data of my
>>> peptide says that the proline is in trans. I am kind of new to the
>>> field.
>>> Please guide me to resolve the problem...
>>>
>>> Thanking you,...
>>> Regards
>>> Deepti Lele
>>>
>>>
>>> --
>>>
>>>
>>>
>>
>>
>>
> --
> Dr. Adrian E. Roitberg
> Associate Professor
> Quantum Theory Project
> Department of Chemistry
>
> Senior Editor. Journal of Physical Chemistry
> American Chemical Society
>
> University of Florida PHONE 352 392-6972
> P.O. Box 118435 FAX 352 392-8722
> Gainesville, FL 32611-8435 Email adrian_at_qtp.ufl.edu
>
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-- 
_______________________________________________
Brent P. Krueger phone: 616 395 7629
Associate Professor fax: 616 395 7118
Hope College Schaap Hall 2120
Department of Chemistry
Holland, MI 49423

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