Dear Ibrahim,
> I have built my dipeptide (Lysine-fructose). and I used RESP ESP charge
> derived server to assign the atomic charges. Please, I used xleap to add
> the same fructose moiety to the lysine residue in my protein and added the
> charges and atom types to this fructose part manually. Of course, I loaded
> both of leaprc.ff99SB and Glycam_06h. Now I get both top and crd files but
> I do not know if these steps are Ok or no. please can you help me.
This is difficult to help with so little information...
-> I guess you generated a dipeptide for this Lysine-fructose and used
R.E.D. Server to generate a central fragment for this modified
dipeptide. May be you could provide in your email the 'PXXXX' R.E.D.
Server name so that we can more easily assist you by looking at your
R.E.D. Server job.
To generate a central fragment for your modified dipeptide see:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#15
To generate the N-term, C-term + central fragments manually, see:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
To generate these 3 fragments automatically see:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
key points here:
- is chemical equivalencing correctly defined in the P2N input file?
See
http://q4md-forcefieldtools.org/REDS/news.php#2
- what is/are the conformation(s) involved in charge derivation for
your dipeptide with this Lysine-fructose?
- what is the algorithm used in MEP computation considering that you
use two different force fields which are based on different MEP
computation algorithm (Connolly surface vs CHELPG). To simplify all
that for this fructose-based central fragment of Lys, you might be
interested in an approach we develop for a-1,4 Glc oligomers:
see
http://www.ncbi.nlm.nih.gov/pubmed/21792425 : the main idea in
this paper is to provide a highly consistent approach for force field
development for glycopeptides; however only tested for a-1,4 Glc based
oligomers. this means that if you decide to follow this approach you
will have to validate it (in all the cases you always have to validate
your approach; so no difference...)
-> then at the end R.E.D. Server/R.E.D. IV provides a mol2 file or a
series of mol2 files that you have to load in LEaP. Here you need to
decide which force field(s) you plan to use and define the
corresponding atom types. Personally I always add these atom types
manually because I want to control my choices.
-> finally you load all the FF libs, define the head/tails (to connect
them where they should be connected) in the LEaP program and generate
the prmtop/prmcrd files; if force field parameters are missing LEaP
will generate errors/the listing of these missing parameters; this
means you have to generate a frcmod file; once again I always generate
this frcmod file by hand to control my choices. See for instance:
the R.E.DD.B. project in relation with the publication above
http://q4md-forcefieldtools.org/REDDB/projects/F-85/
the definition of head/tail and FF atom types
http://q4md-forcefieldtools.org/REDDB/projects/F-85/script1.ff
the frcmod file
http://q4md-forcefieldtools.org/REDDB/projects/F-85/script3.ff
I hope this helps...
regards, Francois
> On Thu, Jan 24, 2013 at 9:51 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
>
>> Dear Ibrahim,
>>
>> > I am trying to simulate the Schiff base for my protein in which
>> > lysine is binding the fructose molecule through a covalent bond NZ-C1 of
>> > fructose. Can I use xleap to build this structure and how. What I have in
>> > my hand that I should separate lysine residue from the protein and attach
>> > it to fructose and then re-ligate, is it correct. I do not know how can
>> > xleap can do.
>>
>> If I understand you you are interested in constructing a new residue
>> i.e. a L-lysine connected to D-fructose through an imine bond.
>>
>> You can use R.E.D. and/or R.E.D. Server for this work; and you can
>> directly build a new central fragment for this new Lysine residue.
>> See for instance: http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php
>> &
>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
>> vs
>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
>>
>> You could also consider splitting this 'lys-fructose' residue into two
>> building blocks. You can find examples of such an approach in R.E.DD.B.
>> See for instance in the sugar domain:
>> http://q4md-forcefieldtools.org/REDDB/projects/F-85/
>> http://q4md-forcefieldtools.org/REDDB/projects/F-72/
>> http://q4md-forcefieldtools.org/REDDB/projects/F-71/
>>
>> R.E.D. uses the P2N file format as input described at:
>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#3
>> & generates FF library in the mol2 file format described at:
>> http://q4md-forcefieldtools.org/Tutorial/leap-mol2.php
>> This mol2 file format is directly usable in the LEaP prgram as described
>> at:
>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#1
>>
>> regards, Francois
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Received on Wed Feb 13 2013 - 23:30:03 PST
