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 Universität München
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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Nov 23 2015 - 04:30:03 PST
