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
>>
> _______________________________________________
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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 Thu Aug 18 2011 - 13:00:03 PDT
