Dear Francois,
I have loaded both leaprc.ff12SB and leaprc.GLYCAM_06h for my dipeptide
(Lys-Fru) as non-standard amino acid residue. Then I have loaded the new
FF.lib with the head and tail were defined and the pdb file of the protein
in xleap but I still have a problem with atom type. I got the following
error
Unit Editor: > check x
Unit Editor: Checking 'x'....
Unit Editor: WARNING: The unperturbed charge of the unit: -1.000000 is not
zero.
Unit Editor: Warning: Close contact of 0.930843 angstroms between .R<PHE
11>.A<H 2> and .R<SER 34>.A<HG 9>
Unit Editor: Warning: Close contact of 1.107358 angstroms between .R<TYR
50>.A<H 2> and .R<SER 77>.A<HG 9>
Unit Editor: Warning: Close contact of 1.198180 angstroms between .R<PHE
56>.A<H 2> and .R<GLN 143>.A<HE21 14>
Unit Editor: Warning: Close contact of 1.323347 angstroms between .R<ARG
59>.A<HH11 18> and .R<ARG 59>.A<HD2 12>
Unit Editor: Warning: Close contact of 1.004213 angstroms between .R<PHE
98>.A<H 2> and .R<SER 123>.A<HG 9>
Unit Editor: Warning: Close contact of 1.432209 angstroms between .R<ARG
99>.A<HE 15> and .R<ARG 99>.A<HB2 6>
Unit Editor: Warning: Close contact of 1.378498 angstroms between .R<TYR
134>.A<HH 15> and .R<ARG 168>.A<HE 15>
Unit Editor: Warning: Close contact of 0.982326 angstroms between .R<TYR
139>.A<H 2> and .R<SER 166>.A<HG 9>
Unit Editor: Checking parameters for unit 'x'.
Unit Editor: Checking for bond parameters.
Unit Editor: Checking for angle parameters.
Unit Editor: Could not find angle parameter: CT - NT - Cg
Unit Editor: There are missing parameters.
Unit Editor: check: Warnings: 9
Unit Editor: Unit is OK.
> quit
Unfotunately I can not find this angle parameter. Please, any suggestions
will be appreciated. Please I attached both my dipeptide (FLY.off) and a
pdb file for protein (protein.pdb).
Best Regards,
Ibrahim
On Fri, Feb 22, 2013 at 9:17 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> 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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- application/octet-stream attachment: FLY.off
Received on Tue Feb 26 2013 - 11:00:03 PST
