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

From: Maral Aminpour <>
Date: Thu, 19 Mar 2015 13:35:39 -0600

Dear Francois,

Thank you very much for the links. Please find attached a figure of my peptide with C8H17 and CH3 non-standard residues.



On Mar 18, 2015, at 3:07 AM, FyD <> wrote:

> 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?
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Thu Mar 19 2015 - 13:00:04 PDT
Custom Search