Re: AMBER: Trans proline

From: Adrian Roitberg <>
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.


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 <> 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
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
Received on Wed Jul 23 2008 - 06:07:06 PDT
Custom Search