Re: AMBER: Trans proline

From: Adrian Roitberg <roitberg.qtp.ufl.edu>
Date: Sun, 20 Jul 2008 08:27:45 -0400

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.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.qtp.ufl.edu
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Received on Wed Jul 23 2008 - 06:07:06 PDT