Hi Lachele,
>From the references on webpage
http://glycam.ccrc.uga.edu/ccrc/pages/cite.html, I did not find a
comprehensive description of GLYCAM 04 force field. I really want to know
the differences between GLYCAM 06 and GLYCAM04 in terms of application. So
generally speaking, GLYCAM04 is more specific for carbohydrates while
GLYCAM06 is more comprehensive for various types of organic molecules? Does
it follow that for a system of protein and carbohydrate mixture, we should
use either GLYCAM06 solely or, say, GLYCAM04 + ff99SB ?
In addition, I understand that GLYCAM04EP force field would better simulate
a system with plenty of hydrogen bond interactions. But if I am just
simulating a carbohydrate ligand with a protein receptor, would there be any
benefit by using, say, GLYCAM04EP + ff99SB force fields?
What about glycam04EP.dat + parm99EP.dat? How much would be the increase in
computational costs when we are accounting for these extra points?
Thanks,
Yun
On Fri, Sep 9, 2011 at 7:52 AM, Lachele Foley (Lists) <lf.list.gmail.com>wrote:
> The URL below contains a listing of papers relevant to GLYCAM
> development. The methods are all described in these papers or the
> papers contain references to their descriptions.
>
> http://glycam.ccrc.uga.edu/ccrc/pages/cite.html
>
> You shouldn't be terribly concerned that different methods were used
> in the charge derivation. Of course, it is always good to ask. Amino
> acids and monosaccharides are chemically distinct species; so,
> depending on the model, the proper methods for devlopment might differ
> for each.
>
> The type CG was introduced for this very reason: monosaccharides,
> because of their complexity, cannot easily be modeled using the same
> atom types as are used in amino acids. In each molecular class, the
> tetrahedral carbon atoms exist within different environments. But,
> the difference isn't necessarily in their van der Waals parameters. If
> you inspect the files Glycam_06g.dat and parm99.dat found in
> $AMBERHOME/dat/leap/parm, you will find that the vdW terms are exactly
> the same for CG and CT. Instead, the CG type was defined so that
> distances, angles and torsions could be developed so that they are
> specific to carbohydrates but so that they do not overlap with
> existing (and working!) parameters for other molecule classes.
>
> The intention is that the differences make the non-bonded interactions
> more closely represent reality than they might otherwise. Of course,
> these force fields are constantly evolving, and that evolution is
> driven by the fact that models are always approximations to reality
> (otherwise they would be reality...), and approximations, by
> definition, do not contain all information. What I mean by this is
> that you should always find some way to validate any computational
> technique you wish to employ.
>
> :-) Lachele
>
>
> On Fri, Sep 9, 2011 at 2:38 AM, Yun Shi <yunshi09.gmail.com> wrote:
> > Hi Lachele,
> >
> > It helps a lot!
> >
> > Since I am studying the interaction between a protein and a ligand with
> > carbohydrate moiety, I am also concerned about the non-bonded parameters.
> >
> > Although both ff99SB and GLYCAM used RESP charges, but it seems different
> > methods were utilized in charge derivation. I recalled it's Connolly
> surface
> > algorithm vs CHELPG algorithm. And I guess charge constraints were
> applied
> > during the GLYCAM RESP charge derivation. I wonder what constraints in
> > detail were used and how charges were derived for central fragments
> > (building blocks) instead of a holistic molecule. Could you please direct
> me
> > to some papers to read?
> >
> > In addition, I guess the VDW parameters for, i.e., atom type CG in GLYCAM
> > are different from atom type CT in ff99SB. Could you tell me where to
> find
> > the vdw parameters for GLYCAM atom types?
> >
> > So in the end, to what extend would these differences between GLYCAM and
> > ff99SB affect non-bonded interaction?
> >
> > Thanks,
> >
> > Yun
> >
> > On Tue, Aug 30, 2011 at 2:01 PM, Lachele Foley (Lists) <
> lf.list.gmail.com>wrote:
> >
> >> I will reword what you say to be a little more precise, just to be sure.
> >>
> >> * For any given sequence of four bonded atom types (note "types"),
> >> bonded as A-B-C-D, anywhere within a single simulation, there should
> >> be only set of torsion parameters (one "torsion term"). Each torsion
> >> term consists of one or more sub-sets (each also a "term")
> >> representing one or more torsional periodicities. Note that D-C-B-A
> >> is equivalent to A-B-C-D. If more than one torsion term is specified,
> >> the behavior of the system depends primarily on the order in which the
> >> multiply-specified terms were read. This latter situation should be
> >> avoided.
> >>
> >> * For any given sequence of two bonded atom types (again, note
> >> "types"), P-R, anywhere within a single simulation, one or more
> >> torsion terms might contribute to the behavior of P, R and their
> >> immediate bonded neighbors. Because the atoms P and R will frequently
> >> be at least sp2 hybridized, there will often be more than one relevant
> >> torsion term.
> >>
> >> Consider ClBrHC-CHClBr -- the C-C bond will have only one
> >> bond-stretching term describing it. However, for example, the average
> >> distance observed between the two carbons will be influenced by
> >> interactions between the Cl, Br and H atoms attached to each carbon
> >> (van der Waals and electrostatic). These interactions, in turn, will
> >> be influenced by all the relevant A-B-C-D torsions (Cl-C-C-Cl,
> >> Cl-C-C-Br, Cl-C-C-H, Br-C-C-Br, Br-C-C-H, H-C-C-H -- I think I got
> >> them all...). Have we mentioned angle parameters yet? Those count,
> >> too. :-)
> >>
> >> Note, also, that the carbon type in the example above will very likely
> >> be different from the carbon type for a carbon in another environment,
> >> say in an ester or an aromatic ring.
> >>
> >> Does that help?
> >>
> >> :-) Lachele
> >>
> >> On Tue, Aug 30, 2011 at 4:24 PM, Yun Shi <yunshi09.gmail.com> wrote:
> >> > Hi Lachele,
> >> >
> >> > I just want to clarify on this.
> >> >
> >> > So for a given atomic sequence (within a specific ligand), there is
> ONLY
> >> ONE
> >> > dihedral term (which may be single or multiple)? And for a given bond,
> >> there
> >> > might be (and will be in many cases since there are many sp3 carbons)
> a
> >> > couple of dihedral terms?
> >> >
> >> > Thanks,
> >> >
> >> > Yun
> >> >
> >> > On Mon, Aug 29, 2011 at 4:56 PM, Lachele Foley (Lists) <
> >> lf.list.gmail.com>wrote:
> >> >
> >> >> Where there is a multiple torsion term, that multiple term is applied
> >> >> only to the atomic sequence(s) to which it applies. However, there
> >> >> might be several single and/or multiple terms that are relevant to a
> >> >> given bond.
> >> >>
> >> >> Glycam and ff99SB both employ the amber functional form. The only
> >> >> difference is in treatment of electrostatic and non-bonded 1-4
> >> >> interactions. In ff99SB, these are scaled according to the default
> >> >> values for amber. In glycam, they are not scaled.
> >> >>
> >> >>
> >> >> On Mon, Aug 29, 2011 at 7:03 PM, Yun Shi <yunshi09.gmail.com> wrote:
> >> >> > Hi Lachele,
> >> >> >
> >> >> > I read from the *Torsion Parameters* part of the GLYCAM06 paper
> that
> >> for
> >> >> a
> >> >> > given bond, i.e., C1 - Ox, all involved atomic sequences, including
> O5
> >> -
> >> >> C1
> >> >> > -Ox - Cx, C2 - C1 -Ox - Cx, and H1 - C1 - Ox - Cx have their
> >> respective
> >> >> > torsion terms defined.
> >> >> >
> >> >> > But I wonder if multiple torsion terms (i.e. a 2-fold term plus a
> >> 3-fold
> >> >> > term) are applied to ONE atomic sequence.
> >> >> >
> >> >> > In addition, I did not find the functional forms (potential energy
> >> >> > equations) for GLYCAM force field. Are them identical to the one
> used
> >> in
> >> >> > amber99SB force field?
> >> >> >
> >> >> > Thanks,
> >> >> >
> >> >> > Yun
> >> >> >
> >> >> > On Thu, Aug 18, 2011 at 12:47 PM, Lachele Foley (Lists)
> >> >> > <lf.list.gmail.com>wrote:
> >> >> >
> >> >> >> The entries in the prep files are the correct ones to begin with
> for
> >> >> >> any given residue. Of course, during a simulation, they will
> change
> >> >> >> (unless restrained, of course). The values in the parameter file
> are
> >> >> >> based on small molecules. For larger molecules, the value of any
> >> >> >> given bond length, angle or torsion will depend on the combined
> >> >> >> effects of all the individual pieces, including electrostatics and
> >> van
> >> >> >> der Waals contributions. The values in the prep file take into
> >> >> >> account these combined effects.
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> On Thu, Aug 18, 2011 at 3:18 PM, Yun Shi <yunshi09.gmail.com>
> wrote:
> >> >> >> > So for example, I saw in the GLYCAM_06.prep file
> >> >> >> >
> >> >> >> > ...
> >> >> >> >
> >> >> >> > 22 C6 CG 3 19 15 11 1.540 109.2 -179.8 0.0230
> >> >> >> > 23 H61 HC E 22 19 15 1.070 109.5 60.1 0.0000
> >> >> >> > 24 H62 HC E 22 19 15 1.070 109.5 -179.9 0.0000
> >> >> >> > 25 H63 HC E 22 19 15 1.070 109.5 -59.9 0.0000
> >> >> >> >
> >> >> >> > ...
> >> >> >> >
> >> >> >> > which indicates the CG-HC bond length in a rhamnose residue is
> >> 1.070
> >> >> A.
> >> >> >> But
> >> >> >> > in the Glycam_06g.dat file,
> >> >> >> >
> >> >> >> > ...
> >> >> >> >
> >> >> >> > CG-HC 340.0 1.090 Parm94
> >> >> >> > ...
> >> >> >> >
> >> >> >> > it is 1.090 angstrom. So which one should be correct? Or which
> one
> >> >> would
> >> >> >> be
> >> >> >> > used as I load a rhamnose residue in tleap?
> >> >> >> >
> >> >> >> > Thanks,
> >> >> >> >
> >> >> >> > Yun
> >> >> >> >
> >> >> >> >
> >> >> >> > On Thu, Aug 18, 2011 at 11:54 AM, Lachele Foley (Lists)
> >> >> >> > <lf.list.gmail.com>wrote:
> >> >> >> >
> >> >> >> >> The distances, etc., in the prep file are optimized for the
> whole
> >> >> >> >> residue. If you want to see the individual bond, angle,
> torsion
> >> >> >> >> (etc.) parameters, you need the parameter file. The most
> recent
> >> >> >> >> version for glycam is Glycam_06g.dat. You can find these and
> >> other
> >> >> >> >> parameters in $AMBERHOME/dat/leap/parm
> >> >> >> >>
> >> >> >> >>
> >> >> >> >> On Thu, Aug 18, 2011 at 2:03 PM, Yun Shi <yunshi09.gmail.com>
> >> wrote:
> >> >> >> >> > Hi Bill and Lachele,
> >> >> >> >> >
> >> >> >> >> > Thank you very much. So dummy atoms exist just because
> internal
> >> >> >> >> coordinates
> >> >> >> >> > system instead of Cartesian coordinates system is used.
> >> >> >> >> >
> >> >> >> >> > I think the GLYCAM prep file contains all the sugar building
> >> >> blocks,
> >> >> >> and
> >> >> >> >> I
> >> >> >> >> > just want to dig all the parameters from the prep file.
> >> >> >> >> >
> >> >> >> >> > But since there are ideal bond lengths, angles, and dihedral
> >> angles
> >> >> >> >> > parameters, where can I find the corresponding values of
> force
> >> >> >> constants
> >> >> >> >> as
> >> >> >> >> > in the functional forms (potential energy equations) of amber
> >> force
> >> >> >> >> field?
> >> >> >> >> >
> >> >> >> >> >
> >> >> >> >> > Yun
> >> >> >> >> >
> >> >> >> >> >
> >> >> >> >> > On Wed, Aug 17, 2011 at 7:09 PM, Lachele Foley (Lists) <
> >> >> >> >> lf.list.gmail.com>wrote:
> >> >> >> >> >
> >> >> >> >> >> The prep file format is a little confusing at first.
> >> >> >> >> >>
> >> >> >> >> >> > But I do not understand what are those first three DUMM
> atoms
> >> >> for?
> >> >> >> >> >>
> >> >> >> >> >> Those set the coordinate space.
> >> >> >> >> >>
> >> >> >> >> >> > What -0.1940 stands for?
> >> >> >> >> >>
> >> >> >> >> >> The manual recommends not using this number at all, so in
> >> Glycam
> >> >> prep
> >> >> >> >> >> entries, we use the space as a convenient location indicate
> the
> >> >> total
> >> >> >> >> >> charge on the residue. And, we don't use it for any other
> >> >> purpose.
> >> >> >> >> >>
> >> >> >> >> >> > What are the letters and numbers from 4th to 7th columns
> >> mean?
> >> >> >> >> >>
> >> >> >> >> >> Of these, only column 4 is used. 5-7 are completely ignored
> by
> >> >> most
> >> >> >> >> >> programs (this is stated in the docs). The numbers are,
> >> >> essentially,
> >> >> >> >> >> comments regarding the atoms to which the bonds, angles and
> >> >> torsions
> >> >> >> >> >> apply. However, since they are never used, any incorrect
> >> entries
> >> >> in
> >> >> >> >> >> those columns are unlikely to have ever been caught. The
> atoms
> >> to
> >> >> >> >> >> which the bond lengths, angles and torsions are applied must
> be
> >> >> >> >> >> deduced by inspecting the contents of column 4. To
> understand
> >> >> column
> >> >> >> >> >> 4, go see the page that Bill referenced. If you're a CS
> >> person, I
> >> >> am
> >> >> >> >> >> told that if you consider it a stack, and you count up from
> the
> >> >> >> >> >> bottom, the entries in column 4 are a bit easier to make
> sense
> >> of.
> >> >> >> >> >>
> >> >> >> >> >> :-) Lachele
> >> >> >> >> >>
> >> >> >> >> >>
> >> >> >> >> >> On Wed, Aug 17, 2011 at 9:34 PM, Bill Ross <
> ross.cgl.ucsf.edu>
> >> >> >> wrote:
> >> >> >> >> >> >> Or could anyone just direct me to the right documentation
> to
> >> >> read?
> >> >> >> >> >> >
> >> >> >> >> >> > Searching google for 'amber prep file':
> >> >> >> >> >> >
> >> >> >> >> >> > http://ambermd.org/doc/prep.html
> >> >> >> >> >> >
> >> >> >> >> >> > Bill
> >> >> >> >> >> >
> >> >> >> >> >> > _______________________________________________
> >> >> >> >> >> > AMBER mailing list
> >> >> >> >> >> > AMBER.ambermd.org
> >> >> >> >> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >> >> >> >
> >> >> >> >> >>
> >> >> >> >> >>
> >> >> >> >> >>
> >> >> >> >> >> --
> >> >> >> >> >> :-) Lachele
> >> >> >> >> >> Lachele Foley
> >> >> >> >> >> CCRC/UGA
> >> >> >> >> >> Athens, GA USA
> >> >> >> >> >>
> >> >> >> >> >> _______________________________________________
> >> >> >> >> >> AMBER mailing list
> >> >> >> >> >> AMBER.ambermd.org
> >> >> >> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >> >> >>
> >> >> >> >> > _______________________________________________
> >> >> >> >> > AMBER mailing list
> >> >> >> >> > AMBER.ambermd.org
> >> >> >> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >> >> >
> >> >> >> >>
> >> >> >> >>
> >> >> >> >>
> >> >> >> >> --
> >> >> >> >> :-) Lachele
> >> >> >> >> Lachele Foley
> >> >> >> >> CCRC/UGA
> >> >> >> >> Athens, GA USA
> >> >> >> >>
> >> >> >> >> _______________________________________________
> >> >> >> >> AMBER mailing list
> >> >> >> >> AMBER.ambermd.org
> >> >> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >> >>
> >> >> >> > _______________________________________________
> >> >> >> > AMBER mailing list
> >> >> >> > AMBER.ambermd.org
> >> >> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >> >
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> --
> >> >> >> :-) Lachele
> >> >> >> Lachele Foley
> >> >> >> CCRC/UGA
> >> >> >> Athens, GA USA
> >> >> >>
> >> >> >> _______________________________________________
> >> >> >> AMBER mailing list
> >> >> >> AMBER.ambermd.org
> >> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >>
> >> >> > _______________________________________________
> >> >> > AMBER mailing list
> >> >> > AMBER.ambermd.org
> >> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >> >
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> :-) Lachele
> >> >> Lachele Foley
> >> >> CCRC/UGA
> >> >> Athens, GA USA
> >> >>
> >> >> _______________________________________________
> >> >> AMBER mailing list
> >> >> AMBER.ambermd.org
> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >>
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >>
> >>
> >>
> >> --
> >> :-) Lachele
> >> Lachele Foley
> >> CCRC/UGA
> >> Athens, GA USA
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
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Received on Wed Sep 14 2011 - 17:00:02 PDT
