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

From: Maral Aminpour <aminpour.gmail.com>
Date: Fri, 20 Mar 2015 20:27:15 -0600

Sorry. I donít know whatís wrong with it. I attached it again as a zip file.







> On Mar 20, 2015, at 12:03 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> Attachment not included.
>
> Bill
>
> <div>-------- Original message --------</div><div>From: Maral Aminpour <aminpour.gmail.com> </div><div>Date:03/20/2015 10:51 AM (GMT-08:00) </div><div>To: AMBER Mailing List <amber.ambermd.org> </div><div>Subject: Re: [AMBER] Non-Standard Residue / Non-Integer Charge </div><div>
> </div>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 - 19:30:02 PDT
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