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 Fri Sep 16 2011 - 04:00:03 PDT
