Replying to the list so this info is more generally available in case
others wonder.
The files look ok best I can tell without digging really deeply. The
GLYCAM force field does have some negative amplitudes in the dihedral
terms. So, it is certainly possible to have negative dihedral values.
This is a small effect, and the presence of protein or other residues
usually make it so that the overall values are negative. But, this
file is just an oligosaccharide in water. Water has no dihedrals, so
no dihedral terms. And, the specific oligosaccharide contains some of
the atom types that can have negative values in their associated
dihedrals. I didn't check every dihedral individually (because that's
a lot of work), but I think it's ok that you have negative DIHED
values. If you're really worried, try using parmtop utilities in
AmberTools too look closely at all the dihedrals. Those tools work
well.
Maybe ask the gamd folks if they can make it possible for negative
dihedral energies not to cause trouble?
It might not be a problem anyway. Consider the amount of the effect
compared to what gamd does. If you are trying to increase sampling,
you're probably already messing with the energy function. If the
DIHED values are small compared to other bonded energies, it might not
make a lot of difference to the outcome, depending on exactly what
gamd is doing. Keep in mind that dihedral energies are just
corrections to the other bonded terms, at least in the GLYCAM
philosophy.
On Tue, Apr 9, 2019 at 1:32 PM Lachele Foley <lf.list.gmail.com> wrote:
>
> Send it to my personal email (lf.list.gmail.com).
>
> On Tue, Apr 9, 2019 at 3:56 AM Rajarshi Roy <phd1701171011.iiti.ac.in> wrote:
> >
> > Dear Mam,
> > Did you receive the topology file? In amber mailing list is not allowing me
> > to send those files because of the size issue.
> >
> > On Tue, Apr 9, 2019 at 9:13 AM Rajarshi Roy <phd1701171011.iiti.ac.in>
> > wrote:
> >
> > > Dear Mam,
> > > I am not still able to figure it out. I am simulating a proteoglycan chain
> > > only. So there is no protein part. My chain just consists of dermatan
> > > sulphate only. Please check my topology and coordinate files. I am not able
> > > to find any error or discrepancy in output files or by visualization.
> > > Thank you in advance
> > >
> > > On Mon, Apr 8, 2019 at 9:20 PM Lachele Foley <lf.list.gmail.com> wrote:
> > >
> > >> Also... I'm pretty sure they shouldn't be negative. So, I might need
> > >> a lot of details.
> > >>
> > >> If you already figured it out, just let us know.
> > >>
> > >> On Mon, Apr 8, 2019 at 11:24 AM Lachele Foley <lf.list.gmail.com> wrote:
> > >> >
> > >> > Sorry to take so long to respond. There's lots going on.
> > >> >
> > >> > Can you tell me more molecular details about your system?
> > >> > Specifically, how large is the 'proteo' part and how large is the
> > >> > 'glycan' part? Feel free to send the input prmtop and inpcrd to me
> > >> > (to just me is fine). Thanks!
> > >> >
> > >> > On Tue, Apr 2, 2019 at 7:05 AM Rajarshi Roy <phd1701171011.iiti.ac.in>
> > >> wrote:
> > >> > >
> > >> > > Dear AMBER user and developers,
> > >> > > I am trying to simulate a proteoglycan structure using conventional
> > >> > > molecular dynamics technique. Everything seems to be fine in the
> > >> output
> > >> > > file where only the dihedral energy is showing a negative value. So
> > >> why am
> > >> > > I getting the negative value in dihedral energy? Is there any
> > >> discrepancy
> > >> > > in my system?
> > >> > > Secondly, when I am trying to simulate the same system using amd or
> > >> gamd in
> > >> > > dual boost mode, but dihedral boost potential remains zero throughout
> > >> our
> > >> > > simulation. As discussed in the gamd archive it is because of the
> > >> negative
> > >> > > dihedral energy.
> > >> > > So is it an error to get negative dihedral energy or can I use the
> > >> single
> > >> > > potential boost in amd or gamd technique?
> > >> > > It will be beneficial for me if you clarify all these doubts.
> > >> > > Thank you in advance!
> > >> > >
> > >> > > --
> > >> > > *with regards*
> > >> > >
> > >> > > *Rajarshi Roy*
> > >> > >
> > >> > >
> > >> > > *PhD Research Scholar*
> > >> > >
> > >> > > *Biosciences and Biomedical Engineering*
> > >> > >
> > >> > > *Indian Institute of Technology, Indore*
> > >> > > *India*
> > >> > > _______________________________________________
> > >> > > AMBER mailing list
> > >> > > AMBER.ambermd.org
> > >> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >> >
> > >> >
> > >> >
> > >> > --
> > >> > :-) Lachele
> > >> > Lachele Foley
> > >> > CCRC/UGA
> > >> > Athens, GA USA
> > >>
> > >>
> > >>
> > >> --
> > >> :-) Lachele
> > >> Lachele Foley
> > >> CCRC/UGA
> > >> Athens, GA USA
> > >>
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > >
> > >
> > > --
> > > *with regards*
> > >
> > > *Rajarshi Roy*
> > >
> > >
> > > *PhD Research Scholar*
> > >
> > > *Biosciences and Biomedical Engineering*
> > >
> > > *Indian Institute of Technology, Indore*
> > > *India*
> > >
> >
> >
> > --
> > *with regards*
> >
> > *Rajarshi Roy*
> >
> >
> > *PhD Research Scholar*
> >
> > *Biosciences and Biomedical Engineering*
> >
> > *Indian Institute of Technology, Indore*
> > *India*
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Wed Apr 10 2019 - 12:30:03 PDT
