Re: [AMBER] Negative dihedral angle n glycan simulation

From: Lachele Foley <>
Date: Mon, 8 Apr 2019 11:24:16 -0400

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 <> 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

:-) Lachele
Lachele Foley
Athens, GA USA
AMBER mailing list
Received on Mon Apr 08 2019 - 08:30:02 PDT
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