[gmx-users] placing dihedral constraints

[Mark Abraham]

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 /<Mark.Abraham at anu.edu.au>/* wrote:
>
>
>     From: Mark Abraham <Mark.Abraham at anu.edu.au>
>     Subject: Re: [gmx-users] placing dihedral constraints
>     To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>     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
>
>     -----Inline Attachment Follows-----
>
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