Dear Francois,
I Still have one more question (probably). I am trying to link my dipeptide
(LYS-FRU fragment) back into my protein. In the protein, LYS residue is in
the second position and when load my pdb file into xleap an extra OXT atom
automatically added to the first residue and two hydrogen atoms to the the
third residue.
I am using the following script for LYS-FRU Fragment:
./xleap -s -f leaprc.ff12SB
glycam_06 = loadamberparams GLYCAM_06h.dat
X = loadmol2 X.mol2
set X head X.1.N
set X tail X.1.C16
set X.1 connect0 X.1.N
set X.1 connect1 X.1.C16
set X.1 restype saccharide
set X.1 name "mol"
set X.1.C1 type CG
.
.
.
set X.1.H62 type H1
then I loaded my protein into xleap. Now, How can I bind the LYS-FRU to the
2nd and 3rd residues (the preceding and the following residues).
Regards, Francois
Ibrahim
On Sun, Feb 17, 2013 at 2:38 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Ibrahim,
>
> > 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.
>
> You ran a big job and automatically generated FF libraries for the
> N-term, C-term & central fragments + the corresponding dipeptide
> according to the tutorial at:
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
>
> Yes, a lot of files were generated:
> http://cluster.q4md-forcefieldtools.org/~.../Project/P2909.html
> this is normal you get lost ;-)
>
> All the files generated by R.E.D. Server are described at:
> http://q4md-forcefieldtools.org/Tutorial/P2N/All-frag-Pept/listing-6mol.pdf
> see page 5: you really need:
> mm1-o1.FG2.mol2 Central fragment: Molecule 1 – conformation 1 (Fragment 2)
> mm3-o1-FG.mol2 N-terminal fragment: Molecule 3 – conformation 1
> mm5-o1-FG.mol2 C-terminal fragment: Molecule 5 – conformation 1
> mm6-o1.mol2 Molecule 6 – conformation 1
> & likely only:
> mm1-o1.FG2.mol2 Central fragment: Molecule 1 – conformation 1 (Fragment 2)
>
> The key P2N file is the first one of the six files:
> http://cluster.q4md-forcefieldtools.org/~.../Project/P2909/Mol_red1.p2n
> -> chemical equivalencing was generated by Ante_R.E.D. 2.0 -> all is ok:
> http://q4md-forcefieldtools.org/REDS/news.php#2
>
> REMARK Information automatically added by R.E.D. Server
> REMARK INTRA-MCC 0.0000 | 1 2 3 4 5 6 | Remove
> REMARK INTRA-MCC 0.0000 | 49 50 51 52 53 54 | Remove
> -> this is to define the central fragment
>
> REMARK INTER-MCC 0.0000 | 2 3 | 1 2 3 4 | 1 2 3 4 5 6 7 8
> REMARK INTER-MCC 0.0000 | 4 5 | 1 2 3 4 | 47 48 49 50 51 52 53 54
> -> this is to define the N-term & C-term fragments between molecules
> 2-3 & 4-5
>
> the RRMS of the RESP fit with chemical equivalencing and all the
> charge constraints:
>
> http://cluster.q4md-forcefieldtools.org/~.../Project/P2909/Data-R.E.D.Server/Mol_MM/output2_mm
>
> ESP relative RMS (SQRT(chipot/ssvpot)) 0.03331
>
> the RRMS of the 1st RESP stage without chemical equivalencing and
> without the charge constraints:
>
> http://cluster.q4md-forcefieldtools.org/~.../Project/P2909/Data-R.E.D.Server/Mol_MM/stat-output-b_mm
>
> ESP relative RMS (SQRT(chipot/ssvpot)) 0.02964
>
> -> the difference 0.033-0.030 is pretty good...
>
> You can also look at local/charge errors:
>
> http://cluster.q4md-forcefieldtools.org/~.../Project/P2909/Data-R.E.D.Server/Mol_MM/stat-RESP-FIT_mm
> -> the errors are mainly observed for N-term & C-term fragments; this
> is normal...
>
> You decided to use 'pop=mk' for all your data; I think this is the
> most simple; at least in a first approach:
>
> http://cluster.q4md-forcefieldtools.org/~.../Project/P2909/Data-R.E.D.Server/Mol_m1/JOB2-gau_m1-1-1.com
>
> The key to finish to check your RESP charge derivation data:
> do you like the conformation obtained after geometry optimization?:
> See the java applet :
>
> http://cluster.q4md-forcefieldtools.org/~.../Project/P2909/javaappletpdb-1.html
> The peptide backbone looks like to be in an extended conformation;
> concerning the fructose part (http://en.wikipedia.org/wiki/Fructose),
> the conformation is not 4C1
> (http://web.inc.bme.hu/csonka/csg/glc/glc.htm); only you should know
> what conformation you want for this fructose part: it should be close
> to your experimental data or close to a choice you voluntary made!
>
> I hope this helps...
>
> regards, Francois
>
>
> > 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 Thu Feb 21 2013 - 09:00:03 PST
