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
>
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Received on Tue Aug 30 2011 - 13:30:03 PDT
