Dear Ibrahim,
> 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.
OXT means C-terminal and consequently means last residue; not first one...
If OXT is automatically added by LEaP this means it is missing in the
C-terminal fragment in your PDB file: you have to check that...
More generally once LEaP has identified a residue (i.e. match between
a FF lib & a residue from a PDB file) LEaP automatically adds the
missing atoms (missing in the PDB file if any) based on these defined
in the FF lib.
> 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
-> I would define atom names in the new FF library that means
'something'; i.e. CA for alpha carbon by analogy to the other residues
available in the Amber force field topology database (& in particular
with the regular LYS residue).
This should allow you to more easily identify atoms when displaying a
structure in a graphical program and when using ptraj you will be able
to use * and ? cards for instance all the CA atoms...
> 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).
Jason has just answered to this question in an another email:
Let's count this LYS-FRU residue as the i residue: once the head/tail
are defined in the FF lib the connection between the pairs of residues
"i-1 - i" and "i - i+1" are automatic.
- You load all the Amber FF lib in LEaP
- You load your new FF lib with head/tail defined
- You load the PDB file (exp. data)
- Residues are recognized if the atom & residue names are identical in
the PDB file & FF lib
- Connections between pairs of residues is carried out if the
head/tail are defined for all the residues
regards, Francois
> 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 - 23:30:03 PST
