Hi Francois,
I have attached another charge constraints scheme here. So do you mean I
should derive charges from both fashions, and then calculate the average
charges for each atoms?
Sorry I still cannot find the database version of Glycam04 and glycam06
within the cyclodextrin paper and its Supporting information.
Thanks,
Yun
On Fri, Sep 16, 2011 at 3:42 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Yun,
>
> > 1.
> > Please see attached my charge-derivation scheme for one of the
> thiol-linked
> > 'glycopeptides', where I have two red intermolecular charge constraints
> and
> > one blue intra-molecular charge constraint set to 0.
>
> ok
>
> You might also try per-OH-methyl-glycoside versions instead of the
> hemiacetal monosaccharide units...
>
> > I will have 2 conformations for each sugar molecule respectively, and
> maybe
> > 3 for the modified TRP. Does this look OK?
>
> ok - if you care you will have to choose among various set of
> intra-monosaccharide hydrogen bonds...
>
> > I will follow the so-called
> > multi-molecule multi-conformation approach?
>
> ok
>
> > 2.
> > Which .dat version of GLYCAM04 was used for developing q4md-CD and
> testing
> > in the cyclodextrin paper? And GLYCAM06 version?
>
> I think the GLYCAM versions used/compared are reported in the manuscript.
>
> See also the F-85 R.E.DD.B. project
> . http://q4md-forcefieldtools.org/REDDB/projects/F-85/
> + its leaprc script + frcmod file:
> http://q4md-forcefieldtools.org/REDDB/projects/F-85/script1.ff
> http://q4md-forcefieldtools.org/REDDB/projects/F-85/script3.ff
>
> > 3.
> > I tried deriving charges with R.E.D. server for one molecule. Without any
> > constraint, I found that the total charge of every single atom within
> this
> > molecule is 0.0004 e. Is this normal?
>
> The RESP program generates charge values with 6 digits after the
> decimal point; the rounding off procedure to get charge values with 4
> digits is responsible for this 0.0000 +/-0.000X error.
>
> > It seems the RRMS value can be used to see how close the derived charges
> fit
> > the ESP, but where should I find this value when running charge
> derivation
> > with R.E.D. server?
>
> See the RESP output: I just ran a RESP-C2 demonstration job for a 10
> molecule jobs .
> http://q4md-forcefieldtools.org/REDS/RED-Server-demo1.php
>
> The data are .
>
> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFaEsVIQjKADFDv89a14yM0ugjuejf03srADF/P3540.html
>
> The RESP output (single RESP stage fitting procedure) for the 10
> molecule charge derivation is .
>
> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFaEsVIQjKADFDv89a14yM0ugjuejf03srADF/P3540/Data-R.E.D.Server/Mol_MM/output1_mm
>
> the RRMS value is:
> ESP relative RMS (SQRT(chipot/ssvpot)) 0.18989
>
> regards, Francois
>
>
> > On Tue, Sep 13, 2011 at 8:46 AM, FyD <fyd.q4md-forcefieldtools.org>
> wrote:
> >
> >> Yun,
> >>
> >> > And GLYCAM used different charges for alpha and beta anomers, so
> should I
> >> > stick to this even if I am using the 'amber' strategy?
> >>
> >> You do not 'need' to stick to this: you simply use two different
> >> building blocks: one is alpha and the other is beta; in these
> >> conditions, this is normal that by fitting to the MEP you get two
> >> different charge values for the alpha and beta anomers...
> >>
> >> regards, Francois
> >>
> >>
> >> > On Mon, Sep 12, 2011 at 11:32 PM, Yun Shi <yunshi09.gmail.com> wrote:
> >> >
> >> >> Hi Francois,
> >> >>
> >> >> I am worried since I saw no atom names information in the gaussian
> input
> >> >> file, which I used to do geometry optimization. I guess I should
> >> construct
> >> >> the gaussian input file from the xxx.pdb file generated by
> Ante_R.E.D.,
> >> then
> >> >> do my geometry optimization, then submit the gaussian out file
> together
> >> with
> >> >> xxx.p2n for charge derivation. So would there be any problem by doing
> >> so?
> >> >>
> >> >> In addition, I have only two major conformations for my small test
> >> molecule
> >> >> after QM geometry optimizations. So I wonder if I could just
> construct a
> >> >> merged p2n file with pdb coordinates from the two major QM-optimized
> >> >> conformers? I don't quite understand why R.E.D. server need QM
> >> optimization
> >> >> output file.
> >> >>
> >> >> Looking through the 'q4md-CD' paper, I feel it kind of
> counter-intuitive
> >> to
> >> >> mix GLYCAM04 geometrical parameters with atomic charges from 'Amber'
> >> >> strategy, which however, reproduced experimental data so well. But
> now I
> >> >> feel like that the RESP charges come hand-in-hand with the scaling
> >> factor,
> >> >> and I guess using the amber scaling factors is the major reason that
> >> your
> >> >> charge-derivation approach is successful.
> >> >>
> >> >> Since my molecule (the thio-glycosidic part) has no reference to look
> >> for
> >> >> experimental data to compare, what would be a simple experiment to
> carry
> >> out
> >> >> to validate my parameters? Or just try fitting them to QM
> calculations?
> >> >>
> >> >> By the way, what do you mean by " 'recompute' key dihedrals" when
> taking
> >> >> parameters from GAFF? And which are key dihedrals?
> >> >>
> >> >> Thanks,
> >> >>
> >> >> Yun
> >> >>
> >> >>
> >> >>
> >> >> On Wed, Sep 7, 2011 at 11:57 PM, FyD <fyd.q4md-forcefieldtools.org>
> >> wrote:
> >> >>
> >> >>> Dear Yun,
> >> >>>
> >> >>> > I basically understand this approach now. But for this
> >> >>> Rha-S-CH2-CH(R)-NH-
> >> >>> > group, how should I deal with the N terminus? If I simply add an
> ACE
> >> cap
> >> >>> to
> >> >>> > make it Rha-S-CH2-CH(R)-NH-ACE,
> >> >>>
> >> >>> Yes, with a trans peptide bond:
> >> >>>
> >> >>> H
> >> >>> Rha-S-CH2-CH(R)-N-C-Me
> >> >>> O
> >> >>>
> >> >>> > then how to set charge constraints?
> >> >>>
> >> >>> You set a single INTRA-MCC = 0 for the ACE chemical group in the P2N
> >> file.
> >> >>>
> >> >>> See http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#15
> >> >>> (However in this #15 example two capping groups are added, so two
> >> >>> INTRA-MCC are set in the P2N file; In your case, you need to set a
> >> >>> single INTRA-MCC in your P2N file).
> >> >>>
> >> >>> > Should I
> >> >>> > add a Met or a Hydrogen to O3 on Rha? Because CENTRAL fragments
> >> instead
> >> >>> of
> >> >>> > TERMINNAL fragments are needed here.
> >> >>>
> >> >>> So you need two L-Rhamnoside building blocks...
> >> >>> a perOH-thiomethyl-Rhamnoside & a perOH-O-methyl-Rhamnoside
> >> >>>
> >> >>> [You could also try a different set of connecting groups between
> >> >>> S/O-hemiacetals (instead of S/O-acetals) and methoxy groups (i.e.
> >> >>> ether groups instead of hydroxyl groups).
> >> >>>
> >> >>> > Sorry our library does not have access to the Cieplak et al.
> paper.
> >> >>>
> >> >>> ok, I will send you the pdf file to your personal address (I think
> the
> >> >>> license to publish exclude the free distribution of this paper)...
> >> >>>
> >> >>> > In addition, I noted that GLYCAM06 have exactly the same charges
> for
> >> >>> most
> >> >>> > atoms in the same sugar molecule with different linkage, i.e.,
> >> >>> > 2-L-alpha-Rhamnose share identical atomic charges with
> >> >>> 3-L-alpha-Rhamnose
> >> >>> > except O2 and O3. However in amber99sb, every corresponding single
> >> atom
> >> >>> of,
> >> >>> > say TRP, would have different charges from ntTRP. I guess this may
> >> have
> >> >>> > something to do with the charge-deriving methods, as
> qwt=0.0005/0.001
> >> in
> >> >>> > 99sb VS qwt=0.01 in GLYCAM.
> >> >>>
> >> >>> This has to do with the charge constraints applied during the charge
> >> >>> fitting step.
> >> >>>
> >> >>> > But then the question would be, should I set charge constraints to
> >> most
> >> >>> > atoms on the sugar ring except the anomeric carbon and derive
> charges
> >> >>> using
> >> >>> > RESP-C2 for the sugar part, which would allow me to avoid the use
> of
> >> the
> >> >>> > first Rhamnose? Or just do all charges with RESP-A1A?
> >> >>>
> >> >>> Well you are right; this is the key ;-)
> >> >>>
> >> >>> -1- I guess GLYCAM developers will suggest you to use something
> >> >>> similar to the RESP-C2 charge model; i.e. MEP computation using the
> >> >>> CHELPG algo. and a single RESP fitting stage using the qwt=.01
> >> >>> hyperbolic restraint. This means using 1.0 scaling factors for the
> 1-4
> >> >>> non-bonding interactions for the sugar part of your ligand and
> 1.2/2.0
> >> >>> for the other part. Quite complex... considering the size of your
> >> >>> ligand and considering that the Connolly surface algorithm is used
> in
> >> >>> MEP computation and a two RESP stage fitting approach is used for
> the
> >> >>> non-sugar part.
> >> >>>
> >> >>> -2- Considering that L-Rhamnose is the 6-deoxy-L-mannose, I would
> >> >>> follow the approach we described .
> >> >>> http://www.ncbi.nlm.nih.gov/pubmed/21792425/ for all your ligand
> and
> >> >>> more general all your molecular system (in case of a Galacto
> >> >>> configuration I would suggest you to use the GLYCAM approach -1-).
> >> >>> This means 1.2/2.0 scaling factors for all the 1-4 non-bonding
> >> >>> interactions and using the Connolly surface algorithm in MEP
> >> >>> computation and a two RESP stage fitting approach for the entire
> >> >>> ligand. Far more simple... However, this approach has obviously to
> be
> >> >>> validated (however as it is requested for the case -1-).
> >> >>>
> >> >>> regards, Francois
> >> >>>
> >> >>>
> >> >>>
> >> >>> > On Sat, Aug 27, 2011 at 12:16 AM, FyD <
> fyd.q4md-forcefieldtools.org>
> >> >>> wrote:
> >> >>> >
> >> >>> >> Dear Yun,
> >> >>> >>
> >> >>> >> - When you have a peptide bond within a molecule, R1NH-COR2 you
> >> could
> >> >>> >> split this molecule into two parts R1NH-ACE & NME-COR2 (ACE =
> CH3CO;
> >> >>> >> NME = NHCH3; are capping groups). You use two INTRA-MCC set to
> zero
> >> >>> >> for these capping groups:
> >> >>> >>
> >> >>> >> R.E.D.:
> >> >>> >> 2 FG2 fragments LEaP
> >> >>> >> R1NH-ACE + NME-COR2 --> R1NH COR2 -----> R1NH-COR2
> >> >>> >> <=> <=>
> >> >>> >> 2 INTRA-MCC = 0
> >> >>> >>
> >> >>> >>
> >> >>> >> - When you have a disaccharide R'-O-R", you could split it into
> two
> >> >>> >> monosaccharides by using an INTER-MCC set to zero between the
> methyl
> >> >>> >> group of the methylglycoside (building-block 1) and the chosen
> >> >>> >> hydroxyl group belonging to the second monosaccharide unit:
> >> >>> >>
> >> >>> >> R.E.D.:
> >> >>> >> R'O-Me HO-R" 2 FG1 fragments LEaP
> >> >>> >> <-----> ---> R'O R" -----> R'-O-R"
> >> >>> >> 1 INTERMCC = 0
> >> >>> >>
> >> >>> >> by analogy, you could test:
> >> >>> >>
> >> >>> >> R'S-Me HS-R"
> >> >>> >> <-----> ---------------> R'-S-R"
> >> >>> >> 1 INTERMCC = 0
> >> >>> >>
> >> >>> >> With these simples rules you can split your red-blue-red-green
> >> >>> >> molecule into 4 building blocks.
> >> >>> >>
> >> >>> >> These have been defined some time ago; see
> >> >>> >> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php
> >> >>> >> &
> >> >>> >> Cieplak et al. Application of the multimolecule and
> >> >>> >> multiconformational RESP methodology to biopolymers: Charge
> >> derivation
> >> >>> >> for DNA, RNA, and proteins. J. Comput. Chem. 1995, 16, 1357-1377.
> >> >>> >>
> >> >>> >> With R.E.D. Server/R.E.D. IV you can generate all these fragments
> >> into
> >> >>> >> a single R.E.D. job by using the corresponding P2N files and by
> >> >>> >> defining the correct constraints during the charge fitting step.
> >> >>> >> See http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php
> >> >>> >> & http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#29
> >> >>> >>
> >> >>> >> regards, Francois
> >> >>> >>
> >> >>> >>
> >> >>> >> Quoting Yun Shi <yunshi09.gmail.com>:
> >> >>> >>
> >> >>> >> > Sorry that I should have attached this model molecule I want to
> >> study
> >> >>> >> > earlier.
> >> >>> >> >
> >> >>> >> > As you can see, I divide this ligand into four parts, and the
> >> >>> parameters
> >> >>> >> > (atomic charges, bonds, angles, dihedrals, impropers) of the
> red
> >> >>> >> (terminal)
> >> >>> >> > sugar and green ASP can be obtained from GLYCAM and 99SB
> >> >>> respectively.
> >> >>> >> >
> >> >>> >> > But I have to include the glycosidic oxygen between two sugar
> >> rings
> >> >>> in
> >> >>> >> the
> >> >>> >> > blue thio sugar, as this glysicidic oxygen is defined in the
> >> >>> preceding
> >> >>> >> sugar
> >> >>> >> > (the blue thio sugar) instead of the succeeding sugar according
> to
> >> >>> >> GLYCAM.
> >> >>> >> >
> >> >>> >> > I plan to use the approach -2- you mentioned (so that I don't
> need
> >> >>> >> generate
> >> >>> >> > many conformations), but considering my specific case, I wonder
> >> why
> >> >>> not
> >> >>> >> > using
> >> >>> >> >
> >> >>> >> > Me-O3-L-RhamnoS-Me + MeS-CH2CH(R)NH-COMe
> >> >>> >> > <----------------------> <===========>
> >> >>> >> > INTER-MCC=0 INTRA-MCC=0
> >> >>> >> >
> >> >>> >> > , and then remove the Me - Me and MeS - COMe respectively?
> >> >>> >> >
> >> >>> >> > Since the L-Rha and TRP in my case carry only one modified site
> >> >>> compared
> >> >>> >> to
> >> >>> >> > their standard counterparts, should I include charge
> constraints
> >> >>> (keep
> >> >>> >> the
> >> >>> >> > atomic charges) for atoms far away from the modified sites?
> Such
> >> as
> >> >>> C5
> >> >>> >> and
> >> >>> >> > C6 in the thio sugar, and the entire indole ring of the
> modified
> >> TRP?
> >> >>> >> >
> >> >>> >> > Thank you so much!
> >> >>> >> >
> >> >>> >> > Yun
> >> >>> >> >
> >> >>> >> >
> >> >>> >> > On Thu, Aug 25, 2011 at 11:37 PM, FyD <
> >> fyd.q4md-forcefieldtools.org>
> >> >>> >> wrote:
> >> >>> >> >
> >> >>> >> >> Yun,
> >> >>> >> >>
> >> >>> >> >> > Sorry, I just read the tutorial, that is, "Central fragment
> of
> >> a
> >> >>> xxx".
> >> >>> >> >> >
> >> >>> >> >> > So for the modified (C-terminal reduced) amino acid, should
> I
> >> add
> >> >>> a
> >> >>> >> MeCO
> >> >>> >> >> at
> >> >>> >> >> > the N-terminus and MeS at the reduced C-terminus?
> (considering
> >> the
> >> >>> >> >> reduced
> >> >>> >> >> > C-terminus is used to link glycosidic sulfur atom).
> >> >>> >> >> >
> >> >>> >> >> > And for the sugar molecule, should I add a Me cap to
> 3-hydroxyl
> >> >>> group
> >> >>> >> in
> >> >>> >> >> > addition to a methyl group attached to the glycosidic
> sulfur?
> >> >>> (This
> >> >>> >> sugar
> >> >>> >> >> > molecule would fall into the category of central fragment of
> my
> >> >>> >> ligand)
> >> >>> >> >>
> >> >>> >> >> ups I overlooked your problem ;-) You do not have any cysteine
> >> >>> >> residue...
> >> >>> >> >>
> >> >>> >> >> Let's re-do the explanations with your terminal
> molecule/pseudo
> >> >>> >> amino-acid:
> >> >>> >> >>
> >> >>> >> >> -1- you consider the following molecule
> >> >>> >> >>
> >> >>> >> >> Thio-L-Rhamno-CH2CH(R)NH-COMe ; R = CH2-Ph
> >> >>> >> >> <==>
> >> >>> >> >> INTRA-MCC
> >> >>> >> >>
> >> >>> >> >> You only have to set up an intra-molecular charge constraint
> >> >>> >> >> (INTRA-MCC keyword) for the COMe capping group (see <==>
> above).
> >> >>> >> >> See
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#15
> >> >>> >> >>
> >> >>> >> >> R.E.D. will generate a sm fragment (mol2 file) for you.
> >> >>> >> >>
> >> >>> >> >> -2- you split your molecule into two building blocks.
> >> >>> >> >>
> >> >>> >> >> L-RhamnoS-Me + HS-CH2CH(R)NH-COMe
> >> >>> >> >> <-------> <==>
> >> >>> >> >> INTER-MCC INTRA-MCC
> >> >>> >> >>
> >> >>> >> >> See
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#16
> >> >>> >> >> or
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#17
> >> >>> >> >>
> >> >>> >> >> You set up an intra-molecular charge constraint (INTRA-MCC
> >> keyword)
> >> >>> >> >> for the COMe capping group.
> >> >>> >> >> You set up an inter-molecular charge constraint (INTER-MCC
> >> keyword)
> >> >>> >> >> between the methyl group of L-RhamnoS-Me and the thiol group
> of
> >> your
> >> >>> >> >> pseudo terminal amino-acid.
> >> >>> >> >>
> >> >>> >> >> The approach -2- is once again more complex but more
> flexible...
> >> >>> >> >>
> >> >>> >> >> R.E.D. will generate a FG fragment (mol2 file) in the Mol_MM
> >> >>> directory.
> >> >>> >> >>
> >> >>> >> >> Sorry for misunderstanding your problem in my first email.
> >> >>> >> >>
> >> >>> >> >> regards, Francois
> >> >>> >> >>
> >> >>> >> >>
> >> >>> >> >> > On Thu, Aug 25, 2011 at 9:58 AM, Yun Shi <
> yunshi09.gmail.com>
> >> >>> wrote:
> >> >>> >> >> >
> >> >>> >> >> >> Thank you very much!
> >> >>> >> >> >>
> >> >>> >> >> >> I looked at the CD project, and I saw when FFTopDB were
> >> >>> constructed,
> >> >>> >> the
> >> >>> >> >> >> 1-metylated glucose was used to derive RESP charges. So in
> my
> >> >>> >> >> >> thio-glycopeptide case, should I use the sugar molecule
> with a
> >> >>> methyl
> >> >>> >> >> group
> >> >>> >> >> >> attached to the glycosidic sulfur as well?
> >> >>> >> >> >>
> >> >>> >> >> >> What about the modified (C-terminal reduced) amino acid?
> Add
> >> one
> >> >>> >> more
> >> >>> >> >> >> methyl group to the modified C-terminal and acetate to the
> >> >>> >> N-terminal?
> >> >>> >> >> >>
> >> >>> >> >> >> But in the end, what is deposited in the FFTopDB is the
> >> residue
> >> >>> >> without
> >> >>> >> >> the
> >> >>> >> >> >> methyl or acetate cap, right?
> >> >>> >> >> >>
> >> >>> >> >> >> Yun
> >> >>> >> >> >>
> >> >>> >> >> >>
> >> >>> >> >> >>
> >> >>> >> >> >> On Wed, Aug 24, 2011 at 11:38 PM, FyD <
> >> >>> fyd.q4md-forcefieldtools.org
> >> >>> >> >> >wrote:
> >> >>> >> >> >>
> >> >>> >> >> >>> Dear Yun Shi,
> >> >>> >> >> >>>
> >> >>> >> >> >>> > I am trying to understand how this works.
> >> >>> >> >> >>>
> >> >>> >> >> >>> If you look at the data available in the "F-85" R.E.DD.B.
> >> >>> project,
> >> >>> >> you
> >> >>> >> >> >>> will find a x/tLEaP script to construct the CD-based
> >> >>> glycopeptides
> >> >>> >> as
> >> >>> >> >> >>> well as a frcmod file for missing force field parameters
> with
> >> >>> >> comments.
> >> >>> >> >> >>>
> >> http://q4md-forcefieldtools.org/REDDB/projects/F-85/script1.ff
> >> >>> >> >> >>>
> >> http://q4md-forcefieldtools.org/REDDB/projects/F-85/script3.ff
> >> >>> >> >> >>>
> >> >>> >> >> >>> > So instead of combining individual residues in a
> >> >>> building-block
> >> >>> >> >> manner,
> >> >>> >> >> >>> as
> >> >>> >> >> >>> > in the assignment of atomic charges for proteins with
> >> >>> amber99sb,
> >> >>> >> it
> >> >>> >> >> is
> >> >>> >> >> >>> > recommended to consider the ligand as a holistic
> molecule
> >> when
> >> >>> >> >> >>> calculating
> >> >>> >> >> >>> > the RESP charge?
> >> >>> >> >> >>>
> >> >>> >> >> >>> 'recommended'? ;-) ... Personally, I use most of the time
> the
> >> >>> >> building
> >> >>> >> >> >>> block approach whatever if the target 'big' molecule is a
> >> ligand
> >> >>> or
> >> >>> >> a
> >> >>> >> >> >>> nucleic acid/protein/polysacharide.
> >> >>> >> >> >>>
> >> >>> >> >> >>> > I am curious that if I could do things in a
> building-block
> >> >>> >> >> >>> > manner since it can potentially decrease a lot of
> >> >>> computational
> >> >>> >> time
> >> >>> >> >> for
> >> >>> >> >> >>> > geometry optimization.
> >> >>> >> >> >>>
> >> >>> >> >> >>> The building-block approach has many advantages:
> >> >>> >> >> >>> - it potentially "decreases a lot of computational time
> for
> >> >>> geometry
> >> >>> >> >> >>> optimization" as you said.
> >> >>> >> >> >>> - it allows rigorously defining the conformation of each
> >> >>> >> >> >>> building-block and not to use a conformation more or less
> >> >>> randomly
> >> >>> >> >> >>> chosen.
> >> >>> >> >> >>> - it allows avoiding interactions between charges group
> >> during
> >> >>> >> >> >>> geometry optimization in gas phase.
> >> >>> >> >> >>> - it allows the construction of analogs for the target
> >> molecule.
> >> >>> >> >> >>> - it allows the construction of oligomers/polymers for the
> >> >>> target
> >> >>> >> >> >>> molecule.
> >> >>> >> >> >>>
> >> >>> >> >> >>> However, it also has disadvantages:
> >> >>> >> >> >>> - it is complex to set up when one starts, but R.E.D. has
> >> been
> >> >>> >> >> >>> designed for this approach.
> >> >>> >> >> >>> - errors during the charge fitting step are introduced
> when
> >> >>> using
> >> >>> >> the
> >> >>> >> >> >>> building-block approach; these errors have to be minimized
> by
> >> >>> >> >> >>> correctly selecting the connecting groups between the
> >> different
> >> >>> >> >> >>> building-blocks. The statistics module available in R.E.D.
> >> >>> >> >> >>> Server/R.E.D. IV also helps to localize/minimize these
> >> errors.
> >> >>> >> >> >>>
> >> >>> >> >> >>> > And when it comes to geometrical parameters, we should
> use
> >> >>> GLYCAM
> >> >>> >> for
> >> >>> >> >> >>> sugar
> >> >>> >> >> >>> > part, 99SB for standard amino acids, and GAFF for
> organic
> >> >>> part?
> >> >>> >> >> >>>
> >> >>> >> >> >>> Yes
> >> >>> >> >> >>>
> >> >>> >> >> >>> - We only select 'obvious' missing force field parameters
> >> from
> >> >>> GAFF
> >> >>> >> >> >>> (we recompute key dihedrals), and when used we always
> >> >>> rationalize
> >> >>> >> >> >>> these force field parameters as it was done in the Cornell
> at
> >> >>> al.
> >> >>> >> >> >>> force field.
> >> >>> >> >> >>>
> >> >>> >> >> >>> - In this work, we used Amber scaling factor values for
> 1-4
> >> >>> >> >> >>> non-bonding interactions for all the glycopeptide
> molecular
> >> >>> systems;
> >> >>> >> >> >>> i.e. we did not split the system into a peptide and a
> sugar
> >> >>> parts.
> >> >>> >> >> >>>
> >> >>> >> >> >>> > BTW, could you tell me how to generate multiple
> >> conformations
> >> >>> with
> >> >>> >> >> >>> geometry
> >> >>> >> >> >>> > optimization from Gaussian 09?
> >> >>> >> >> >>>
> >> >>> >> >> >>> You could do a conformational search - although if the
> >> >>> >> building-block
> >> >>> >> >> >>> approach is used the conformational search is quite
> >> >>> simplified...
> >> >>> >> >> >>> We also often modify a key dihedral to look for lowest
> >> >>> >> minimum/minima.
> >> >>> >> >> >>>
> >> >>> >> >> >>> To create a P2N file with multiple conformations, see:
> >> >>> >> >> >>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#3
> >> >>> >> >> >>>
> >> >>> >> >>
> >> >>> >>
> >> >>>
> >>
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#EXAMPLE-P2N-FILE
> >> >>> >> >> >>>
> >> >>> >> >> >>> To create a QM file with multiple conformations to be used
> in
> >> >>> the
> >> >>> >> Mode
> >> >>> >> >> >>> 2 of R.E.D. (see
> >> >>> >> >> >>>
> http://q4md-forcefieldtools.org/REDS/popup/popredmodes.php),
> >> >>> simply
> >> >>> >> >> >>> concatenate the different QM outputs into a single file.
> >> >>> >> >> >>>
> >> >>> >> >> >>> regards, Francois
> >> >>> >> >> >>>
> >> >>> >> >> >>> >> Dear Yun,
> >> >>> >> >> >>> >>
> >> >>> >> >> >>> >> > Is it technically possible to do it due diligence in
> the
> >> >>> first
> >> >>> >> >> place?
> >> >>> >> >> >>> >> That
> >> >>> >> >> >>> >> > is, cut the molecule into three parts as I mentioned
> >> >>> before,
> >> >>> >> use
> >> >>> >> >> >>> GLYCAM
> >> >>> >> >> >>> >> for
> >> >>> >> >> >>> >> > the sugar part, 99SB for the Thr, and GAFF for
> modified
> >> Phe
> >> >>> and
> >> >>> >> >> the
> >> >>> >> >> >>> >> > thio-glycosidic linkage. And may I then link these
> parts
> >> >>> >> together
> >> >>> >> >> >>> using
> >> >>> >> >> >>> >> LEaP
> >> >>> >> >> >>> >> > ?
> >> >>> >> >> >>> >>
> >> >>> >> >> >>> >> Concerning the use of GLYCAM + GAFF + Amber99SB you
> might
> >> be
> >> >>> >> >> >>> >> interested by looking at the following paper:
> >> >>> >> >> >>> >> http://www.ncbi.nlm.nih.gov/pubmed/21792425
> >> >>> >> >> >>> >> & its corresponding R.E.DD.B. project .
> >> >>> >> >> >>> >> http://q4md-forcefieldtools.org/REDDB/projects/F-85/ +
> >> its
> >> >>> LEaP
> >> >>> >> >> >>> script:
> >> >>> >> >> >>> >>
> >> >>> http://q4md-forcefieldtools.org/REDDB/projects/F-85/script1.ff
> >> >>> >> >> >>> >>
> >> >>> >> >> >>> >> This work is about cyclodextrin based-glycopeptide and
> 1-4
> >> >>> >> >> non-bonding
> >> >>> >> >> >>> >> interactions in GLYCAM & Amber99SB.
> >> >>> >> >> >>> >>
> >> >>> >> >> >>> >> Your structure is not a cyclodextrin but this work
> >> describe
> >> >>> (i)
> >> >>> >> how
> >> >>> >> >> to
> >> >>> >> >> >>> >> derive charges and build force field libraries for new
> >> >>> fragments
> >> >>> >> by
> >> >>> >> >> >>> >> using R.E.D. IV and (ii) proposes new directions
> >> concerning
> >> >>> the
> >> >>> >> >> >>> >> treatment of 1-4 non-bonding interactions in the
> context
> >> of
> >> >>> >> >> >>> >> glycopeptides.
> >> >>> >> >> >>> >>
> >> >>> >> >> >>> >> Finally, in the LEaP script you will find examples how
> to
> >> >>> connect
> >> >>> >> >> >>> >> organic, amino-acid and monosaccharide units...
> >> >>> >> >> >>> >>
> >> >>> >> >> >>> >> regards, Francois
>
>
>
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Received on Sun Sep 18 2011 - 22:00:03 PDT
