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
>>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Mon Aug 29 2011 - 17:00:03 PDT
