Hi Jason,
This helps tremendously. Thank you very much for the explanation, it makes
sense to me know. Best.
Sid
On Tue, May 6, 2014 at 10:33 AM, Jason Swails <jason.swails.gmail.com>wrote:
> On Tue, 2014-05-06 at 10:04 -0700, Sidney Elmer wrote:
> > Hi all,
> >
> > I am a little nervous about the dihedral terms I just found in one of my
> > prmtop files for a system with DNA (built with the amberff99SB-ILDN force
> > field). Below I show all the dihedrals for a CYT residue (I haven't
> > checked if this problem is occurring in other residues or in other force
> > fields). Note the entries that I have marked '#' or '##' or '###', these
> > are the terms I am questioning. From what I understand, any term that
> > begins with 'E' extends the definition of the dihedral term preceding it.
> > Is that correct? If that's the case, then it would only make sense that
> > the atoms which define the term would have to be exactly the same in each
> > row. Is that correct?
> >
> > If both of my assertions above are correct, then there is a big problem
> > because the dihedrals I have marked '#' or '##' or '###' do not follow
> > those rules. Is this a bug in tleap?
> >
> > If on the other hand, these entries below are allowed, could someone
> please
> > explain to me what they mean, because I am confused if this is designed
> > this way. Thank you for your help.
>
> I'll try to keep this short-ish, but here's some background to start.
> Amber defines both impropers and proper dihedrals in the same list and
> uses the same functional form to treat them. In the prmtop, improper
> dihedrals are indicated with a negative 4th term, whereas
> end-group-ignored dihedrals have a negative 3rd atom index (see
> http://ambermd.org/formats.html). I think rdparm uses "E" to denote
> ignored _E_nd groups and B to denote that _B_oth end-groups are ignored
> AND it is an improper, but don't quote me on the notation there).
>
> The dihedral list is used in the Amber source code as an effective 1-4
> nonbonded pairlist and the 1-4 atom pairs are actually excluded from
> each other in the nonbonded list. Therefore, the prmtop has to indicate
> somewhere in the dihedral list which atoms need to have their 1-4
> interactions computed in the 1-4 nonbonded list and which ones need to
> be omitted.
>
> As you pointed out, multiterm dihedrals (in which all 4 atoms are
> exactly the same) should have at most 1 of their dihedrals have a
> positive 3rd atom index so that you don't calculate the same 1-4
> nonbonded interactions multiple times. For proteins, most of the
> negative indexes mean precisely that -- you have a multiterm dihedral
> and only want to compute the end-group interactions once.
>
> A topological complication arises from rings (6-membered rings and
> smaller). Consider the cartoon below (hopefully you have a fixed-width
> font to view it in):
>
> 2----3
> / \
> 1 4
> \ /
> 5-----6
>
> Atoms 1 and 4 are partners in two dihedrals -- 1-2-3-4 and 1-5-6-4. You
> only want to count those end-groups once, so ONE of those dihedrals
> should be marked with an "E" even though it's not a multi-term dihedral.
>
> Consider 5-membered rings
>
> 2----3
> / \
> 1 4
> \ /
> \_ _/
> 5
>
> Now atoms 1 and 4 are dihedral partners in the 1-2-3-4 torsion, but
> they're also connected by an angle via 1-5-4 and should be excluded
> entirely, so again 1-2-3-4 should be marked "E" even if there is only 1
> term because those atoms are excluded on the basis of being a 1-3 pair.
>
> Rings are far more prevalent in nucleic acids than amino acids
> (obviously), but you will see the same kind of thing with phenylalanine
> or tyrosine, for instance. Note, any ring larger than 7 atoms will not
> have two atoms connected by multiple dihedrals, angles, or bonds (unlike
> 6-, 5-, and 4-membered rings), so only these 3 ring sizes are
> special-cased.
>
> Hope this helped,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Tue May 06 2014 - 11:30:04 PDT
