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

From: Maral Aminpour <aminpour.gmail.com>
Date: Fri, 20 Mar 2015 11:51:14 -0600

Dear Francois,
I attached it to (amber.ambermd.org) email. Thatís how I need to do, right? I 'll attach it again to this email. Sorry, for the inconvenience.
Cheers,
Maral






On Mar 20, 2015, at 12:58 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:

> Quoting Maral Aminpour <aminpour.gmail.com>:
>
>> Thank you very much for the links. Please find attached a figure of
>> my peptide with C8H17 and CH3 non-standard residues.
>
> So Maral, this figure... whereisit? regards, Francois
>
>> On Mar 18, 2015, at 3:07 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
>>
>>> Dear Maral,
>>>
>>> You could try to use PyRED at RED Server Dev.
>>> http://q4md-forcefieldtools.org/REDServer-Development/
>>>
>>> Tutorials are at:
>>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-4.php
>>>
>>> Documentation is at:
>>> http://q4md-forcefieldtools.org/REDServer-Development/Documentation/
>>>
>>> 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:
>>>> (http://sf.anu.edu.au/~vvv900/amber-tutorial/1cgh-nonstandard/index.html).
>>>>
>>>> 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 Fri Mar 20 2015 - 11:00:03 PDT
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