On 7/07/2011 3:29 AM, Mr Bernard Ramos wrote:
Hi Mark and everyone!
This has been a previous topic though and thanks Mark for the reply.
What I need to do is to calculate the potential energy (energy
minimzation) of a molecule at every fixed pairs of dihedrals (phi, psi).
So you really have a problem about creating particular conformations of
peptides, and then doing some EM on them. Your original email didn't say
that, so I wasn't able to give relevant help.
EM is only good for local optimization, so just applying a large force
constant will not necessarily find a sensible minimum that satisfies the
restraint. A stinking mess is a fairly likely result. MD has a better
chance of getting to the region of a minimum you seek, but will still be
fiddly.
A good molecule building program will allow you to rotate the parts of
the molecule about a dihedral to set the value you want. *Then* do EM.
If you hadn't pre-supposed the form of the solution to your underlying
problem, you'd have got what I think is more effective help last time :-)
If you have a lot of conformers to generate, then Google around to see
if there are any useful tools available.
Mark
I did the suggestions on
_http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints_. In
fact what follows is the entry I placed in my topol.top
[ dihedral_restraints ]
; ai aj ak al type label phi dphi kfac power
5 1 40 38 1 1 30 0 1 2
12 40 38 34 1 1 10 0 1 2
I also added the following in my mdp file
dihre = yes
dihre_fc = 10000
I removed disre_tau and nstdihreout as they are no longer needed in
the recent gromacs versions. Unfortunately, after checking the
dihedral angles, they appear to be far from the set value of (phi=30,
psi=10). I understand that we are restraining the angles and not
constraining/fixing them. Is there a way we can have the resulting phi
and psi as close to the required values? I get values 15 degrees away
from the original settings. Your help is greatly appreciated.
One more question. This restraining will not affect the final
potential energy right?
Bernard
--- On *Mon, 6/27/11, Mark Abraham /<[email protected]>/* wrote:
From: Mark Abraham <[email protected]>
Subject: Re: [gmx-users] placing dihedral constraints
To: "Discussion list for GROMACS users" <[email protected]>
Date: Monday, June 27, 2011, 5:38 PM
On 06/27/2011 07:31 PM, Mr Bernard Ramos wrote:
Hi!
I would like to freeze two dihedrals/torsion angles but allow the
rest (i.e. bonds, angles) to relax during energy minimization and
MD. How do I go over applying constraints? Thanks.
See
http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints
to sort out some nomenclature. You probably want a dihedral
restraint with a strong force constant (though other approaches
are possible). See relevant parts of chapters 4 and 5. Work by
analogy from the [dihedrals] and [position_restraints] sections in
your existing [moleculetype].
Mark
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