Re: [AMBER] Non-Standard Residue / Non-Integer Charge

From: FyD <>
Date: Wed, 18 Mar 2015 10:07:46 +0100

Dear Maral,

You could try to use PyRED at RED Server Dev.

Tutorials are at:

Documentation is at:

Providing a drawing or a pdb file for the molecule(s) you are
interested in could help... to help you ;-)

regards, Francois

> I tried to introduce two non-standard residues (Octyl group: C8H17
> and Methyl: CH3) to a peptide sequence in Amber following this
> tutorial:
> (
> I cut the Octyl and Me out of peptide separately and add Nme to them
> to mimic an adjacent amino acid. I calculated the charge of
> Octyl-Nme and Me-Nme using Gaussian program. I assigned the charges
> and atom types to them using antechamber in a way that total charge
> of each (Octyl-Nme and Me-Nme ) is equal to -1. After deleting Nme
> group from them, I also manually edited the charge of carbon atom in
> the octyl and Nme to be sure that I get -1 as the net charge for
> the non-standard residues as a dirty and fast solution. After
> defining the head and tail of the non-standard residues I save off
> the non-standard residue libraries. After loading all libraries,
> missed parameters and pdb file of the peptide including
> non-standard residues, there is no connection between the
> nonstandard residues and the standard residues of the peptide they
> are attached to in xleap. I connected them manually in the xleap
> and saveoff the toatal *.lib file. Now the total charge of the
> peptide is not intege
> r.
> Why I get the non-integer value for the charge of the total system
> after connecting non-standard residues to the structure? And how can
> I get rid of it?

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Received on Wed Mar 18 2015 - 02:30:03 PDT
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