Dear Ibrahim,
> thank you for helping. My R.E.D server name P2890 for Lys-Frupyr file.
You can also use the public account of R.E.D. Server to exchange data
between users; see: http://q4md-forcefieldtools.org/REDS/faq.php#22
(more easy to discuss between users; the account protection is public...)
Now I look at your data (I hided your login):
http://cluster.q4md-forcefieldtools.org/~.../Project/P2890.html
Please, read the tutorials at q4md-forcefieldtools.org; in P2890 you
defined a molecular fragment in your P2N input file to be involved in
quantum chemistry (QM) geometry optimization/MEP computation. A
molecular fragment does NOT exist in QM. Please look at the optimized
geometry obtained after geometry optimization; it looks ugly ;-)
http://cluster.q4md-forcefieldtools.org/~.../Project/P2890/javaappletpdb-1.html
this is normal your input structure is not correct...
You have to define a whole molecule i.e. a capped molecule (dipeptide)
with the ACE & NME chemical groups. See the tutorials I reported in my
previous email...
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#15
Using this dipeptide derivative/whole molecule for your
monosaccharide-based modified amino-acid residue, you have to define
two constraints (intra-mcc keyword) set to zero that are applied
during the charge fitting step and that lead to the molecular fragment
you are interested in (by removing the atoms involved in these 2
intra-mcc)...
At the end R.E.D. generates a Mol_m1-o1-sm.mol2 file (the one you
want) besides the whole molecule version (Mol_m1-o1.mol2)
See
http://q4md-forcefieldtools.org/Tutorial/P2N/Central-frag-Pept/listing-1mol.pdf
then if I look at:
http://cluster.q4md-forcefieldtools.org/~.../Project/P2890/Data-R.E.D.Server/JOB2-gau_m1-1-2.com the Gaussian route contains:
Pop=chelpg
this keyword should not be compatible with the amino-acid part and if
you use Pop=mk it should not be not compatible with the sugar part:
this is why we developed this homogeneous approach reported in the
'F-85' R.E.DD.B. project where Pop=mk is applied for the peptide _and_
the sugar parts...
> Now
> I have the following problems: (1) how can ligate this dipeptide into my
> protein. of course, I need to assign atom types,
you need to define the head & the tail for your molecular fragment
See for instance the script1.ff file in the F-85 R.E.DD.B. project
http://q4md-forcefieldtools.org/REDDB/projects/F-85/script1.ff
> (2) Can I use xleap and
> then add the fructose molecule to lysine residue in my protein manually,
Yes see the script1.ff file once again
> 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.
No - here you directly load the mol2 file (Mol_m1-o1-sm.mol2) in LEaP,
you define its head & tails and its atom types and all is done. You
can also use the mol3 file format:
http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php
See the script1.ff file once again
I hope this helps...
regards, Francois
> 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
>> >>
>> >> regards, Francois
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Received on Fri Feb 15 2013 - 02:00:02 PST
