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 - 00:00:02 PDT
