Re: [AMBER] Can LEaP create peptides with D-amino acids?

From: Carlos Simmerling <carlos.simmerling.gmail.com>
Date: Mon, 23 Nov 2015 08:07:57 -0500

You can also edit the leap libraries to do this automatically. It really
depends on what you are trying to accomplish and what input data you have.
On Nov 23, 2015 7:00 AM, "Marion, Antoine" <antoine.marion.tum.de> wrote:

> Hi,
>
> Actually you can use the flip command to do that in combination with
> sequence.
>
> An example for alanine dipeptide:
>
> ###
> source leaprc.ff14SB
> ala = sequence {ACE ALA NME}
>
> # Save standard L peptide (for comparison)
> savepdb ala 2ala-L.pdb
>
> # Select the chiral carbon(s) to be flipped
> select ala.2.CA
> # Flip selection
> flip ala
> # Save D peptide
> savepdb ala 2ala-D.pdb
>
> quit
> ###
>
>
> Best,
>
> Antoine
>
> ________________________________
> -- Dr. Antoine MARION
> Postdoctoral Research Scientist
>
> Department of Life Sciences
> Theoretical Chemical Biology and Protein Modelling Group
> Technische Universit√§t M√ľnchen
> Emil-Erlenmeyer-Forum 8
> D-85354 Freising-Weihenstephan
> Germany
>
> Phone: +49 (0)8161 71-2271
>
>
>
> ________________________________________
> From: Carlos Simmerling <carlos.simmerling.gmail.com>
> Sent: Monday, November 23, 2015 12:10 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Can LEaP create peptides with D-amino acids?
>
> Yes if you are loading a pdb file, but not by using the sequence command.
> On Nov 23, 2015 3:19 AM, "Yip Yew Mun" <yipy0005.gmail.com> wrote:
>
> > Hi,
> >
> > I wish to ask if LEaP can create peptides with D-amino acids?
> >
> > Thank you. :D
> >
> > Yip Yew Mun (Mr) | PhD Research Scholar | Division of Chemistry &
> > Biological Chemistry
> > School of Physical & Mathematical Sciences | Nanyang Technological
> > University | Singapore 639798
> > Tel: (+65) 97967803 | Email: yipy0010.e.ntu.edu.sg | GMT+8h
> >
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> >
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Received on Mon Nov 23 2015 - 05:30:02 PST
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