Dear Francois
I am thanking in advance. I got the following file for capped Lys-Frupyr
fragment. The RED server name P2909, but I recognized some files active and
others are inactive. Also, I don' t know if these large number of files
indicates the QM run is Ok.
Regards, Ibrahim
On Fri, Feb 15, 2013 at 6:09 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> 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 Sun Feb 17 2013 - 01:30:02 PST
