Re: [AMBER] cyclic peptide

From: FyD <>
Date: Thu, 09 Dec 2010 13:37:43 +0100

Dear Rossella,

> I have to build a cyclic peptide, the two terminals aminoacids are N-PRO and
> C-PHE and they are linked togheter by CO-(CH2)3-NH. So the sequence should
> be:
> ...-PRO-CO-CH2-CH2-CH2-NH-PHE-...
> How can I build it?
> I tried making a linear sequence with ACE-PRO-.....-PHE-NME and then I
> turned (but just with the command draw in the unit editor) an hydrogen of
> ACE in a carbon with the idea of using then the command bond, but probably I
> have instead to create a new unit modified of ACE with the right parameters
> for the new methil group... is it right? and if it's so, how can I create
> this new unit?

I think you need to build a new force field library for the following
molecular fragment: CO-CH2-CH2-CH2-NH
This means you could start from the following whole molecule:

By applying two intra-molecular charge constaints set to zero during
the charge fitting step, you will generate the required molecular

       Whole molecule Fragment
  <--> <-->
   (1) (2)
   (1) & (2): two intra-molecular charge constraints = 0

You could use the R.E.D. III.4 tools or R.E.D. Server where you first
need to prepare a P2N file for the whole molecule & then build the
force field library for the molecular fragment.

See tutorials .

  - PDB file ---> P2N file
  - P2N file ---> Tripos mol2 (i.e. FF library)

See &

  - load the mol2 file in LEaP to associate the FF libraries & the PDB
file of your cyclic peptide

regards, Francois

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Received on Thu Dec 09 2010 - 05:00:02 PST
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