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
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Received on Tue Aug 30 2011 - 14:30:03 PDT
