Ibrahim,
I continue my former email... In case you are interested in the mol3
file format you could have a look at the 'F-93' R.E.DD.B. project by
J. Sanders about peptide nucleic acid; this is an example where the
mol3 file format is used... This simplifies I think a lot the use of
force field libraries and the connections between fragments in the
LEaP program...
See
http://q4md-forcefieldtools.org/REDDB/projects/F-93/
regards, Francois
> thank you for helping. My R.E.D server name P2890 for Lys-Frupyr file. Now
> I have the following problems: (1) how can ligate this dipeptide into my
> protein. of course, I need to assign atom types, (2) Can I use xleap and
> then add the fructose molecule to lysine residue in my protein manually,
> then select this residue and assign both atom types and add charges from
> P2890 file manually. The problem of later is, if I dismessed, I need to
> re-add atom types and charges in xleap. Please, any suggestions.
> On Thu, Feb 14, 2013 at 9:00 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
>
>> 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
>> >>
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Received on Fri Feb 15 2013 - 08:30:02 PST
